|
.T-coffee Tutorial |
Centre National De LA Recherche
scientifique
CENTRO DE REGULACCIO GENOMICA, Barcelona
Cédric Notredame
www.tcoffee.org
T-Coffee:
Cheat Sheet
Tutorial and FAQ
T-Coffee Tutorial
(Version 6.18, August 2008)
T-Coffee, PSI-Coffee
3D-Coffee/Expresso
M-Coffee
R-Coffee
APDB and iRMSD
ă Cédric Notredame, Centro de Regulaccio Genomica and Centre National
de la Recherche Scientifique, France
Getting the Example Files of the Tutorial
Is T-Coffee different from ClustalW?
What T-Coffee Can and Cannot do for you …
Combining Sequences and Structures
Identifying Occurrences of a Motif: Mocca
Preparing Your Data: Reformatting and Trimming With
seq_reformat
Accessing the T-Coffee Reformatting Utility
Dealing with Non-automatically recognized formats
Removing the gaps from an alignment
Changing the case of your sequences
Changing the case of specific residues
Changing the case depending on the score
Protecting Important Sequence Names
Colouring/Editing Residues in an Alignment
Coloring specific types of residues
Coloring a specific residue of a specific sequence
Coloring according to the conservation
Colouring/Editing residues in an Alignment Using a Cache
Preparing a Sequence or Alignment Cache
Coloring an Alignment using a cache
Evaluating an alignment and producing a cache
Evaluating an alignment with T-Coffee
Evaluating the level of conservation with a substitution
matrix
Selectively turn some residues to lower case
Selectively modifying residues
Keeping only the best portion of an alignment
Extracting Portions of Dataset
Extracting The High Scoring Blocks
Extracting Sequences According to a Pattern
Extracting Blocks Within Alignment
Analyzing your Multiple Sequence Alignment
Estimating the diversity in your alignment
Reducing and improving your dataset
Extracting the N most informative sequences
Extracting all the sequences less than X% identical
Forcing Specific Sequences to be kept
Identifying and Removing Outlayers
Translating DNA sequences into Proteins
Back-Translation With the Bona-Fide DNA sequences
Finding the Bona-Fide Sequences for the Back-Translation
Guessing Your Back Translation
Fetching The Sequence of a PDB structure
Adapting extract_from_pdb to your own environment
Manipulating RNA sequences with seq_reformat
Producing a Stockholm output: adding predicted secondary
structures
Producing a consensus structure
Adding a consensus structure to an alignment
Analyzing an alifold secondary structure prediction
Visualizing compensatory mutations
Manipulating Phylogenetic Trees with seq_reformat
Comparing two phylogenetic trees
Building Multiple Sequence Alignments
How to generate The Alignment You Need?
The Main Methods and their Scope
Computing Multiple Sequence Alignments With T-Coffee
Computing Very accurate (but slow) alignments with
PSI-Coffee
A Simple Multiple Sequence Alignment
Aligning Very Large Datasets with Muscle
Aligning Very Large Alignments with Mafft
Aligning Very Large Alignments with T-Coffee
Shrinking Large Alignments With T-Coffee
Modifying the default parameters of T-Coffee
Changing the Substitution Matrix
Comparing Two Alternative Alignments
Can You Guess The Optimal Parameters?
Using All the Methods at the Same Time: M-Coffee
Using Selected Methods to Compute your MSA
Combining pre-Computed Alignments
Aligning One sequence to a Profile
Aligning Many Sequences to a Profile
Aligning Other Types of Sequences
Using Secondary Structure Predictions:
Incorporation of the prediction in the alignment
Using other secondary structure predictions
Combining Sequences and 3D-Structures
If you are in a Hurry: Expresso
Aligning Sequences and Structures
Mixing Sequences and Structures
Aligning Profile using Structural Information
Evaluating Alignments with The CORE index
Computing the Local CORE Index
Computing the CORE index of any alignment
Evaluating an Alignment Using Structural Information:
APDB and iRMSD
How to Efficiently Use Structural Information
Evaluating an Alignment With the iRMSD Package
Evaluating Alternative Alignments
Identifying the most distantly related sequences in your
dataset
Evaluating an Alignment according to your own Criterion
Establishing Your Own Criterion
Integrating External Methods In T-Coffee
What Are The Methods Already Integrated in T-Coffee
Plug-In: Using Methods Integrated in T-Coffee
Modifying the parameters of Internal and External Methods
Direct access to external methods
Customizing an external method (with parameters) for
T-Coffee
Managing a collection of method files
The Mother of All method files…
Plug-Out: Using T-Coffee as a Plug-In
Creating Your Own T-Coffee Libraries
Customizing the Weighting Scheme
Abnormal Terminations and Wrong Results
Q: The
program keeps crashing when I give my sequences
Q: The
default alignment is not good enough
Q: The
alignment contains obvious mistakes
Q: How
many Sequences can t_coffee handle
Q: Can I
prevent the Output of all the warnings?
Q: How
many ways to pass parameters to t_coffee?
Q: How
can I change the default output format?
Q: My
sequences are slightly different between all the alignments.
Q: Is it
possible to pipe stuff OUT of t_coffee?
Q: Is it
possible to pipe stuff INTO t_coffee?
Q: Can I
read my parameters from a file?.
Q: I
want to decide myself on the name
of the output files!!!
Q: I
want to use the sequences in an alignment file
Q: I
only want to produce a library
Q: I
want to turn an alignment into a library
Q: I
want to concatenate two libraries
Q: What
happens to the gaps when an alignment is fed to T-Coffee
Q: I
cannot print the html graphic display!!!
Q: I
want to output an html file and a regular file
Q: I
would like to output more than one alignment format at the same time
Q: Is
T-Coffee the best? Why Not Using Muscle, or Mafft, or ProbCons???
Q: Can
t_coffee align Nucleic Acids ???
Q: I do
not want to compute the alignment.
Q: I
would like to force some residues to be aligned.
Q: I
would like to use structural alignments.
Q: I
want to build my own libraries.
Q: I do
not want to use all the possible pairs when computing the library
Q: I
only want to use specific pairs to compute the library
Q: There
are duplicates or quasi-duplicates in my set
Q: Can I
align sequences to a profile with T-Coffee?
Q: Can I
align sequences Two or More Profiles?
Q: Can I
align two profiles according to the structures they contain?
Q:
T-Coffee becomes very slow when combining sequences and structures
Q: Can I
use a local installation of PDB?
Q: Can I
evaluate alignments NOT produced with T-Coffee?
Q: Can I
Compare Two Alignments?
Q: I am
aligning sequences with long regions of very good overlap
Q: Why
is T-Coffee changing the names of my sequences!!!!
Q: How
Can I Edit my Alignment Manually?
Q: Have
I Improved or Not my Alignment?.
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee t_coffee sample_rnaseq1.fasta -mode rmcoffee
use M-Coffee + secondary structure prediction
----------------------------------------------------------------------------
R-Coffee Consan t_coffee sample_rnaseq1.fasta -mode rcoffee_consan
use rcoffee to combine consan alignments. Accurate and Slow
memory t_coffee sample_aln1.fasta -mode memory
A lot of the stuff presented here emanates form two summer schools that were tentatively called the "Prosite Workshops" and were held in Marseille, in 2001 and 2002. These workshops were mostly an excuse to go rambling and swimming in the callanques. Yet, when we got tired of lazing in the sun, we eventually did a bit of work to chill out. Most of our experiments were revolving around the development of sequence analysis tools. Many of the most advanced ideas in T-Coffee were launched during these fruitful sessions. Participants included Phillip Bucher, Laurent Falquet, Marco Pagni, Alexandre Gattiker, Nicolas Hulo, Christian Siegfried, Anne-Lise Veuthey, Virginie Leseau, Lorenzo Ceruti and Cedric Notredame.
This Document contains two main sections. The first one is a tutorial, where we go from simple things to more complicated and show you how to use all the subtleties of T-Coffee. We have tried to put as many of these functionalities on the web (www.tcoffee.org) but if you need to do something special and highly reproducible, the Command Line is the only way.
This tutorial relies on the assumption that you have installed T-Coffee, version 6.18 or higher.
T-Coffee is a freeware open source running on all Unix-like platforms, including MAC-osX and Cygwin. All the relevant information for installing T-Coffee is contained in the Technical Documentation (tcoffee_technical.doc in the doc directory.)
T-Coffee cannot run on the Microsoft Windows shell. If you need to run T -Coffee on windows, start by installing cygwin (www.cygwin.com). Cygwin is a freeware open source that makes it possible to run a unix-like command line on your Microsoft Windows PC without having to reboot. Cygwin is free of charge and very easy to install. Yet, as the first installation requires downloading substantial amounts of data, you should make sure you have access to a broad-band connection.
In the course of this tutorial, we expect
you to use a unix-like command line shell. If you work on Cygwin, this means
clicking on the cygwin icon and typing commands in the window that appears. If
you don't want to bother with command line stuff, try using the online tcoffee
webserver at: www.tcoffee.org
We encourage you to try all the following examples with your own sequences/structures. If you want to try with ours, you can get the material from the example directory of the distribution. If you do not know where this file leaves or if you do not have access to it, the simplest thing to do is to:
1- download T-Coffee's latest version from www.tcoffee.org (Follow the link to the T-Coffee Home Page)
2- Download the latest distribution
3- gunzip <distrib>.tar.gz
4- tar -xvf <distrib>.tar
5- go into <distrib>/example
This is all you need to do to run ALL the examples provided in this tutorial.
Before going deep into the core of the matter, here are a few words to quickly explain some of the things T-Coffee will do for you.
T-Coffee is a multiple sequence alignment program: given a set of sequences previously gathered using database search programs like BLAST, FASTA or Smith and Waterman, T-Coffee will produce a multiple sequence alignment. To use T-Coffee you must already have your sequences ready.
T-Coffee can also be used to compare alignments, reformat
them or -no-proof:yes'>
Mode Command
============================================================================
Very Fast t_coffee sample_aln1.fasta -mode quickaln
lower -ndiag if the sequences are very similar
----------------------------------------------------------------------------
Regular t_coffee sample_aln1.fasta
use the output.html to estimate the MSA accuracy
----------------------------------------------------------------------------
Very Accurate t_coffee sample_aln1.fasta -mode accurate
slow, combines structures, sequences and profiles
----------------------------------------------------------------------------
M-Coffee t_coffee sample_aln1.fasta -mode mcoffee
combines most of the existing MSA packages
----------------------------------------------------------------------------
3D-Coffee t_coffee sample_aln1.fasta -mode 3dcoffee
uses the structure of your sequences if named with PDBID
----------------------------------------------------------------------------
Expresso t_coffee sample_aln1.fasta -mode expresso
finds structures homologous to your sequences
----------------------------------------------------------------------------
PSI-Coffee t_coffee sample_aln1.fasta -mode psicoffee
enriches your sequence with profile information
----------------------------------------------------------------------------
R-Coffee t_coffee three_cdna.fasta -mode cdna
Mode Command
============================================================================
R-Coffee t_coffee sample_rnaseq1.fasta -mode rcoffee
use the predicted secondary structure of your sequences
----------------------------------------------------------------------------
RM-Coffee