biapps emboss EMBOSSDIR=/bio/mb/emboss/ EMBOSS_ACDROOT=/bio/mb/emboss/share/EMBOSS/acd PLPLOT_LIB=/bio/mb/emboss/share/EMBOSS empath=/bio/mb/emboss/bin/ PATH=/bio/mb/emboss/bin/:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/sbin emboss-packinfo About/EMBOSS TITLE EMBOSS INFO About European Molecular Biology Open Source Suite (EMBOSS) HELP Help http://www.uk.embnet.org/Software/EMBOSS/ version2.2.0 dateFri Feb 1 04:36:47 EST 2002 hostnamedghome-osx reference source ftp://ftp.uk.embnet.org/pub/EMBOSS/EMBOSS-latest.tar.gz working source ftp://iubio.bio.indiana.edu/molbio/emboss/EMBOSS-2.2.0.tar.gz GCG gcg-packinfo About/GCG TITLE GCG INFO About Genetics Computer Group software suite (GCG) HELP Help http://www.gcg.com/ ncbitools NCBI=/bio/mb/ncbi/ncbirc ncbipath=/bio/mb/ncbi/bin/ ncbitools-packinfo About/NCBI Tools TITLE NCBI Tools INFO About National Center for Biotechnology Information(NCBI) Tool Kit. Includes BLAST and related software. HELP Help http://www.ncbi.nih.gov/IEB/ToolBox/ versionDec 2001 dateThu Dec 20 11:43:53 EST 2001 reference source ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/ncbi.tar.gz working source ftp://iubio.bio.indiana.edu/molbio/ncbi/ncbi_tools/ncbi-01dec.tar.gz fasta FASTLIBS=/bio/mb/data/fastalib fastapath=/bio/mb/fasta/bin/ fasta-packinfo About/FastA TITLE The FASTA program package INFO About The FASTA program package, version 3, contains many programs for searching DNA and protein databases and one program (prss3) for evaluating statistical significance from randomly shuffled sequences. Copyright 1988, 1991, 1992, 1994, 1995, 1996, 1999 by William R. Pearson and the University of Virginia. Citations see W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444-2448 (Pearson and Lipman, 1988); W. R. Pearson (1996) "Effective protein sequence comparison" Meth. Enzymol. 266:227-258 (Pearson, 1996); Pearson et. al. (1997) Genomics 46:24-36 (Zhang et al., 1997); Pearson, (1999) Meth. in Molecular Biology 132:185-219 (Pearson, 1999). HELP Help version34t10d3 date4 Jan 2001 reference source ftp://ftp.virginia.edu/pub/fasta/fasta3.shar.Z working source ftp://iubio.bio.indiana.edu/molbio/search/fasta/fasta34t10d3.shar.Z Comparison of FASTA3 programs samplebix sample-packinfo About/Bio App Samples TITLE Bioinformatics Application samples INFO About HELP Help http://iubio.bio.indiana.edu/grid/runner/ clustalw About/Clustal multiple alignment Sequence Alignment/Clustal multiple alignment TITLE Clustal W Alignment INFO About Clustal W Clustal W - for multiple sequence alignment by Des Higgins and colleagues. Clustal W is a general purpose multiple alignment program for DNA or proteins. HELP Help with Clustal W file:/bio/mb/docs/clustalw.txt cap About/CAP contig assembly Sequence Alignment/CAP contig assembly TITLE CAP Contig Assembly INFO About CAP A Contig Assembly Program by Xiaoqiu Huang HELP Help with CAP file:/bio/mb/docs/cap.txt fastdnaml About/FastDNAml Phylogeny/FastDNAml TITLE FastDNAml INFO About FastDNAml A faster DNA maximum likelihood phylogeny estimator. fastDNAml is a program derived from Joseph Felsenstein version 3.3 DNAML (part of his PHYLIP package). Users should consult the documentation for DNAML before using this program. Produced by Gary Olsen, Hideo Matsuda, Ray Hagstrom, and Ross Overbeek. HELP Help with FastDNAml http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html tacg About/tacg Restriction Map/tacg TITLE tacg restriction map HELP Help with tacg http://tacg.sourceforge.net/ INFO About tacg tacg analyzes a DNA sequence for restriction enzyme sites, nucleic acid patterns version 2, by Harry Mangalam bixinfo About/Bix command language TITLE BIX - BioInformatics application/command Xml INFO About bix.DTD - BioInformatics application/command Xml rewrite of clustal.command (BOP structure format) d.gilbert, dec97 rewrite of clustal.html (seqpup) and clustalw.config (seqlab) as general parseable structure for specifying app parameters for use w/ a corba client=server interface magic string for this format is "Content=type: biocompute/command" format key = value key = { structured.value } newlines or ';' separate key=value pairs in a structure values that include white space need to be quoted with "" or '' see bopper.idl and ReadCommand.java for current key words (these may change) key words match fields in the bopper.idl, and are case=insensitive commandKeys = { "id", "transport", "action", "filepath", "parlist", "command" }; parameterKeys = { "id", "label", "value", "ifelseRules", "runSwitch" }; containerKeys = { "required", "parlist" }; choiceKeys = { "multiple", "minToShow", "parlist" }; dataKeys = { "datatype", "dataflow", "filename", "flavor", "data" }; ID values are case=sensitive, unique strings. reference IDs and other variables as $ID $serverurl, $tempdir, and $tempname are variables that are set by server (remote or local) at runtime TITLE, INFO and HELP are special par ids ]]> HELP Help http://iubio.bio.indiana.edu/grid/runner/docs/bix.dtd