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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
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