1INSTALL.PROGRAMS:
2
3The Bioperl-run package has (Bio)perl wrappers written for the following applications:
4
5
61.	Coils - Prediction of Coiled Coil Regions in Proteins
7	Bio::Tools::Run::Coil
8	http://www.ch.embnet.org/software/COILS_form.html
9
102.	EMBOSS Applications - European Molecular Biology Open Software Suite
11	Bio::Tools::Run::EMBOSSApplication
12	http://www.hgmp.mrc.ac.uk/Software/EMBOSS/
13
143.	Eponine - Transcription Start Site finder
15	Bio::Tools::Run::Eponine
16	http://www.sanger.ac.uk/Software/analysis/eponine/
17
184.	FootPrinter - Program that performs phylogenetic footprinting.
19	Bio::Tools::Run::FootPrinter
20	http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput.pl
21
225.	Genewise - Gene prediction program
23	Bio::Tools::Run::Genewise
24	http://www.sanger.ac.uk/software/wise2
25
266.	Genscan - Identification of complete gene structures in genomic DNA
27	Bio::Tools::Run::Genscan
28	http://genes.mit.edu/GENSCAN.html
29
307.	Hmmpfam - search a single sequence against an HMM database
31	Bio::Tools::Run::Hmmpfam
32	http://hmmer.wustl.edu/
33
348.	PISE - Web interfaces for Biological Programs
35	Bio::Tools::Run::PiseApplication
36	http://www-alt.pasteur.fr/~letondal/Pise/
37
389.	Primate - Near exact match finder for short sequence tags.
39	Bio::Tools::Run:::Primate
40	http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/ensembl-nci/?cvsroot=Ensembl
41
4210.	FingerPRINTScan - identify the closest matching PRINTS sequence motif fingerprints in a protein sequence
43	Bio::Tools::Run::Prints
44	http://www.bioinf.man.ac.uk/fingerPRINTScan/
45
4611.	pfscan - scan a protein or DNA sequence with a profile library
47	Bio::Tools::Run::Profile
48	http://www.isrec.isb-sib.ch/software/software.html
49
5012.	Pseudowise - a pseudogene precdiction program, part of the wise2 package
51	Bio::Tools::Run::Pseudowise
52	http://www.sanger.ac.uk/software/wise2
53
5413.	RepeatMasker - screens DNA sequences in fasta format against a library of repetitive elements
55	Bio::Tools::Run::RepeatMasker
56	http://repeatmasker.genome.washington.edu
57
5814.	Seg - Identify low-complexity regions in protein sequences
59	Bio::Tools::Run::Seg
60	ftp://ftp.ncbi.nih.gov/pub/seg/
61
6215.	Signalp - predicts the presence and location of signal peptide cleavage sites in amino acid sequences
63	Bio::Tools::Run::Signalp
64	http://www.cbs.dtu.dk/services/SignalP/
65
6616.	Tmhmm - Prediction of transmembrane helices in proteins
67	Bio::Tools::Run::Tmhmm
68	http://www.cbs.dtu.dk/services/TMHMM/
69
7017.	TribeMCL - Method for clustering proteins into related groups.
71	Bio::Tools::Run::TribeMCL
72	http://www.ebi.ac.uk/research/cgg/tribe/
73
7419.	Molphy - MOLecular PHYlogenetics Package
75	Bio::Tools::Run::Molphy
76	http://www.ism.ac.jp/software/ismlib/softother.e.html
77
7820.	Phylip - Suite of Phylogenetics programs (Version 3.6)
79	Bio::Tools::Run::Phylip
80	http://evolution.genetics.washington.edu/phylip.html
81
8222.	DBA - DNA Block Aligner
83	Bio::Tools::Run::Alignment::DBA
84	http://www.sanger.ac.uk/software/wise2
85
8623.	Sim4 - Align CDNA to genomic sequences
87	Bio::Tools::Run::Alignment::Sim4
88	http://globin.cse.psu.edu/
89
9025.     BLAST - Basic Local Alignment Search Tool
91        Bio::Tools::Run::StandAloneBlast (in bioperl-live CVS repository)
92        ftp://ftp.ncbi.nih.gov/blast/executables
93
9426.     FASTA,SSEARCH - Pairwise sequence alignment
95        Bio::Tools::Run::StandAloneFasta
96        ftp://ftp.virginia.edu/pub/fasta
97
9827.     Promoterwise - Sequence alignment designed
99        for promoter sequences
100        http://www.sanger.ac.uk/software/wise2
101
10228.     Lagan - Lagan suite of tools including MLAGAN
103        http://lagan.stanford.edu/
104
10529.     Vista - Visualizing global DNA  sequence alignments of arbitrary length
106        http://www-gsd.lbl.gov/vista/VISTAdownload2.html
107
10830.     Exonerate - A package of alignment tools for protein and EST to genome/DNA alignments
109        http://www.ebi.ac.uk/~guy/exonerate/
110
11131.     AMAP- Protein multiple alignment based sequence annealing
112        http://bio.math.berkeley.edu/amap/
113
11432.     Blat - An alignment tool like BLAST, but structured differently
115        http://genome.ucsc.edu/cgi-bin/hgBlat
116
117
118