INSTALL.PROGRAMS

   1 INSTALL.PROGRAMS:
   2
   3 The Bioperl-run package has (Bio)perl wrappers written for the following applications:
   4
   5
   6 1.      Coils - Prediction of Coiled Coil Regions in Proteins
   7         Bio::Tools::Run::Coil
   8         http://www.ch.embnet.org/software/COILS_form.html
   9
  10 2.      EMBOSS Applications - European Molecular Biology Open Software Suite
  11         Bio::Tools::Run::EMBOSSApplication
  12         http://www.hgmp.mrc.ac.uk/Software/EMBOSS/
  13
  14 3.      Eponine - Transcription Start Site finder
  15         Bio::Tools::Run::Eponine
  16         http://www.sanger.ac.uk/Software/analysis/eponine/
  17
  18 4.      FootPrinter - Program that performs phylogenetic footprinting.
  19         Bio::Tools::Run::FootPrinter
  20         http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput.pl
  21
  22 5.      Genewise - Gene prediction program
  23         Bio::Tools::Run::Genewise
  24         http://www.sanger.ac.uk/software/wise2
  25
  26 6.      Genscan - Identification of complete gene structures in genomic DNA
  27         Bio::Tools::Run::Genscan
  28         http://genes.mit.edu/GENSCAN.html
  29
  30 7.      Hmmpfam - search a single sequence against an HMM database
  31         Bio::Tools::Run::Hmmpfam
  32         http://hmmer.wustl.edu/
  33
  34 8.      PISE - Web interfaces for Biological Programs
  35         Bio::Tools::Run::PiseApplication
  36         http://www-alt.pasteur.fr/~letondal/Pise/
  37
  38 9.      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
  42 10.     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
  46 11.     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
  50 12.     Pseudowise - a pseudogene precdiction program, part of the wise2 package
  51         Bio::Tools::Run::Pseudowise
  52         http://www.sanger.ac.uk/software/wise2
  53
  54 13.     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
  58 14.     Seg - Identify low-complexity regions in protein sequences
  59         Bio::Tools::Run::Seg
  60         ftp://ftp.ncbi.nih.gov/pub/seg/
  61
  62 15.     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
  66 16.     Tmhmm - Prediction of transmembrane helices in proteins
  67         Bio::Tools::Run::Tmhmm
  68         http://www.cbs.dtu.dk/services/TMHMM/
  69
  70 17.     TribeMCL - Method for clustering proteins into related groups.
  71         Bio::Tools::Run::TribeMCL
  72         http://www.ebi.ac.uk/research/cgg/tribe/
  73
  74 18.     PAML - Phylogenetic Analysis by Maximum Likelihood package
  75         Bio::Tools::Run::PAML
  76         http://abacus.gene.ucl.ac.uk/software/paml.html
  77
  78 19.     Molphy - MOLecular PHYlogenetics Package
  79         Bio::Tools::Run::Molphy
  80         http://www.ism.ac.jp/software/ismlib/softother.e.html
  81
  82 20.     Phylip - Suite of Phylogenetics programs (Version 3.6)
  83         Bio::Tools::Run::Phylip
  84         http://evolution.genetics.washington.edu/phylip.html
  85
  86 21.     Clustalw -  general purpose multiple sequence alignment program for DNA or proteins
  87         Bio::Tools::Run::Alignment::Clustalw
  88         http://www.ebi.ac.uk/clustalw/
  89
  90 22.     DBA - DNA Block Aligner
  91         Bio::Tools::Run::Alignment::DBA
  92         http://www.sanger.ac.uk/software/wise2
  93
  94 23.     Sim4 - Align CDNA to genomic sequences
  95         Bio::Tools::Run::Alignment::Sim4
  96         http://globin.cse.psu.edu/
  97
  98 24.     Tcoffee - Multiple Sequence Alignment Package
  99         Bio::Tools::Run::Alignment::Tcoffee
 100         http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
 101
 102 25.     BLAST - Basic Local Alignment Search Tool
 103         Bio::Tools::Run::StandAloneBlast (in bioperl-live CVS repository)
 104         ftp://ftp.ncbi.nih.gov/blast/executables
 105
 106 26.     FASTA,SSEARCH - Pairwise sequence alignment
 107         Bio::Tools::Run::StandAloneFasta
 108         ftp://ftp.virginia.edu/pub/fasta
 109
 110 27.     Promoterwise - Sequence alignment designed
 111         for promoter sequences
 112         http://www.sanger.ac.uk/software/wise2
 113
 114 28.     Lagan - Lagan suite of tools including MLAGAN
 115         http://lagan.stanford.edu/
 116
 117 29.     Vista - Visualizing global DNA  sequence alignments of arbitrary length
 118         http://www-gsd.lbl.gov/vista/VISTAdownload2.html
 119
 120 30.     Exonerate - A package of alignment tools for protein and EST to genome/DNA alignments
 121         http://www.ebi.ac.uk/~guy/exonerate/
 122
 123 31.     AMAP- Protein multiple alignment based sequence annealing
 124         http://bio.math.berkeley.edu/amap/
 125
 126 32.     Blat - An alignment tool like BLAST, but structured differently
 127         http://genome.ucsc.edu/cgi-bin/hgBlat
 128
 129