INSTALL.PROGRAMS:

The Bioperl-run package has (Bio)perl wrappers written for the following applications:


1.	Coils - Prediction of Coiled Coil Regions in Proteins 
	Bio::Tools::Run::Coil
	http://www.ch.embnet.org/software/COILS_form.html

2.	EMBOSS Applications - European Molecular Biology Open Software Suite 
	Bio::Tools::Run::EMBOSSApplication
	http://www.hgmp.mrc.ac.uk/Software/EMBOSS/

3.	Eponine - Transcription Start Site finder
	Bio::Tools::Run::Eponine
	http://www.sanger.ac.uk/Software/analysis/eponine/

4.	FootPrinter - Program that performs phylogenetic footprinting. 
	Bio::Tools::Run::FootPrinter
	http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput.pl

5.	Genewise - Gene prediction program
	Bio::Tools::Run::Genewise
	http://www.sanger.ac.uk/software/wise2

6.	Genscan - Identification of complete gene structures in genomic DNA
	Bio::Tools::Run::Genscan
	http://genes.mit.edu/GENSCAN.html

7.	Hmmpfam - search a single sequence against an HMM database  
	Bio::Tools::Run::Hmmpfam
	http://hmmer.wustl.edu/

8.	PISE - Web interfaces for Biological Programs
	Bio::Tools::Run::PiseApplication
	http://www-alt.pasteur.fr/~letondal/Pise/

9.	Primate - Near exact match finder for short sequence tags.
	Bio::Tools::Run:::Primate
	http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/ensembl-nci/?cvsroot=Ensembl

10.	FingerPRINTScan - identify the closest matching PRINTS sequence motif fingerprints in a protein sequence
	Bio::Tools::Run::Prints
	http://www.bioinf.man.ac.uk/fingerPRINTScan/

11.	pfscan - scan a protein or DNA sequence with a profile library 
	Bio::Tools::Run::Profile
	http://www.isrec.isb-sib.ch/software/software.html	

12.	Pseudowise - a pseudogene precdiction program, part of the wise2 package
	Bio::Tools::Run::Pseudowise
	http://www.sanger.ac.uk/software/wise2 

13.	RepeatMasker - screens DNA sequences in fasta format against a library of repetitive elements 
	Bio::Tools::Run::RepeatMasker
	http://repeatmasker.genome.washington.edu

14.	Seg - Identify low-complexity regions in protein sequences
	Bio::Tools::Run::Seg
	ftp://ftp.ncbi.nih.gov/pub/seg/

15.	Signalp - predicts the presence and location of signal peptide cleavage sites in amino acid sequences	
	Bio::Tools::Run::Signalp
	http://www.cbs.dtu.dk/services/SignalP/

16.	Tmhmm - Prediction of transmembrane helices in proteins
	Bio::Tools::Run::Tmhmm
	http://www.cbs.dtu.dk/services/TMHMM/

17.	TribeMCL - Method for clustering proteins into related groups.
	Bio::Tools::Run::TribeMCL
	http://www.ebi.ac.uk/research/cgg/tribe/

18.	PAML - Phylogenetic Analysis by Maximum Likelihood package
	Bio::Tools::Run::PAML
	http://abacus.gene.ucl.ac.uk/software/paml.html

19.	Molphy - MOLecular PHYlogenetics Package
	Bio::Tools::Run::Molphy
	http://www.ism.ac.jp/software/ismlib/softother.e.html

20.	Phylip - Suite of Phylogenetics programs (Version 3.6)
	Bio::Tools::Run::Phylip
	http://evolution.genetics.washington.edu/phylip.html

21.	Clustalw -  general purpose multiple sequence alignment program for DNA or proteins
	Bio::Tools::Run::Alignment::Clustalw
	http://www.ebi.ac.uk/clustalw/

22.	DBA - DNA Block Aligner 
	Bio::Tools::Run::Alignment::DBA
	http://www.sanger.ac.uk/software/wise2

23.	Sim4 - Align CDNA to genomic sequences
	Bio::Tools::Run::Alignment::Sim4
	http://globin.cse.psu.edu/

24.	Tcoffee - Multiple Sequence Alignment Package
	Bio::Tools::Run::Alignment::Tcoffee
	http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html

25.     BLAST - Basic Local Alignment Search Tool
        Bio::Tools::Run::StandAloneBlast (in bioperl-live CVS repository)
        ftp://ftp.ncbi.nih.gov/blast/executables

26.     FASTA,SSEARCH - Pairwise sequence alignment
        Bio::Tools::Run::StandAloneFasta
        ftp://ftp.virginia.edu/pub/fasta

27.     Promoterwise - Sequence alignment designed
        for promoter sequences
        http://www.sanger.ac.uk/software/wise2

28.     Lagan - Lagan suite of tools including MLAGAN
        http://lagan.stanford.edu/

29.     Vista - Visualizing global DNA  sequence alignments of arbitrary length
        http://www-gsd.lbl.gov/vista/VISTAdownload2.html

30.     Exonerate - A package of alignment tools for protein and EST to genome/DNA alignments
        http://www.ebi.ac.uk/~guy/exonerate/

31.     AMAP- Protein multiple alignment based sequence annealing
        http://bio.math.berkeley.edu/amap/

32.     Blat - An alignment tool like BLAST, but structured differently
        http://genome.ucsc.edu/cgi-bin/hgBlat


