LAST: Genome-Scale Sequence Comparison
======================================

LAST finds similar regions between sequences, and aligns them.  It is
designed for comparing large datasets to each other (e.g. vertebrate
genomes and/or large numbers of DNA reads).  It can:

* Indicate the (un)ambiguity of each column in an alignment.
* Use sequence quality data in a rigorous fashion.
* Align DNA to proteins with frameshifts.
* Compare PSSMs to sequences.
* Calculate the likelihood of chance similarities between random
  sequences.
* Do split and spliced alignment.
* Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

Requirements
------------

To handle mammalian genomes, it's best if you have at least 10-20
gigabytes of real memory, but you can get by with 2 gigabytes.

To install the software, you need a C++ compiler.  On Linux, you might
need to install a package called "g++".  On Mac, you might need to
install command-line developer tools.  On Windows, you might need to
install Cygwin.

Setup
-----

Using the command line, go into the top-level LAST directory.  To
compile the programs, type::

  make

You might get some harmless warning messages.  If your compiler is
really old, you might get an error message like this::

  unrecognized command line option "-std=c++11"

In that case, you can compile like this (which will disable
multi-threading)::

  make CXXFLAGS=-O3

Or you can specify another compiler like this::

  make CXX=MyOtherCompiler

Install (optional)
------------------

You can copy the programs and scripts to a standard "bin" directory
(using "sudo" to request administrator permissions)::

  sudo make install

Or copy them to your personal bin directory::

  make install prefix=~

You might have to log out and back in before your computer recognizes
the new programs.

Usage
-----

Please see the other files in the doc directory, especially
`<last-tutorial.html>`_.

Detailed info & citation
------------------------

Please see: `<last-papers.html>`_

License
-------

LAST (including the scripts) is distributed under the GNU General
Public License, either version 3 of the License, or (at your option)
any later version.

Website
-------

LAST's website is: http://last.cbrc.jp/

Contact
-------

Questions and feedback are very welcome.  We like to use a **public**
mailing list, so everyone can benefit from the discussion:

  last-align (ATmark) googlegroups (dot) com

Please let us know about any problems, rather than giving up in
disgust.  Feedback is essential for scientific software like this: we
cannot solve problems that we are unaware of, and we cannot make it
useful and convenient without learning how various people actually
(try to) use it.  It is also valuable to hear success stories, so we
know what we are doing right.  Unlike some other software projects, we
will never send rude or mocking replies.

Having said that, we cannot promise to always help.  **If you find an
error, please try to: tell us the LAST version number and exact error
message, and give us some input data and exact commands that trigger
the problem.**

If you do a benchmarking test of LAST, we recommend you contact us to
check you are using it in a suitable way.  The history of
bioinformatics benchmarks shows it is all too easy to get this wrong.
