// Class KeySet 

KeySet : "MBCRR.ace"



 // Class LongText 



 // Class Table 

Table : "Packages"
Title	 "Packages"
Sortcolumn	 1
Colonne	 1 Subtitle "Package"
Colonne	 1 From 1
Colonne	 1 Visible
Colonne	 1 Width 12
Colonne	 1 Optional
Colonne	 1 A_Class "Package"
Colonne	 2 Subtitle "Description"
Colonne	 2 From 1
Colonne	 2 Tag "Description"
Colonne	 2 Visible
Colonne	 2 Width 70
Colonne	 2 Optional
Colonne	 2 A_Class "Text"

Table : "Categories"
Title	 "Categories"
Sortcolumn	 1
Colonne	 1 Subtitle "Package"
Colonne	 1 From 1
Colonne	 1 Visible
Colonne	 1 Width 70
Colonne	 1 Optional
Colonne	 1 A_Class "Category"

Table : "Programs"
Title	 "Program Index"
Sortcolumn	 1
Colonne	 1 Subtitle "Program"
Colonne	 1 From 1
Colonne	 1 Visible
Colonne	 1 Width 20
Colonne	 1 Optional
Colonne	 1 A_Class "Program"
Colonne	 2 Subtitle "Description"
Colonne	 2 From 1
Colonne	 2 Tag "Description"
Colonne	 2 Visible
Colonne	 2 Width 70
Colonne	 2 Optional
Colonne	 2 A_Class "Text"



 // Class TableResult 

TableResult : "Packages"
Format  Package  Text 
Package:"ACeDB"	"Text:\"Object-oriented"
"ARTEMIS"	"DNA sequence annotation"
"CLUSTAL"	"Multiple sequence alignment"
"CONSENSUS"	"Create consensus patterns from unaligned sequences"
"DNA-GUI"	"Gel image analysis and annotation"
"EBI"	"Sequence chromatogram viewer"
"FASTA"	"Pairwise and global similarity searches"
"FASTDNAML"	"Maximum likelihood sequence phylogeny"
"forester"	"Programs and API for phylogeny"
"FSAP"	"Sequence analysis tools"
"GCUA"	"Codon usage analysis"
"GDE"	"Genetic Data Environment"
"GENEPARSER"	"Parse a DNA sequence into introns and exons"
"ISREC"	"Multiple alignment display"
"LINDENBAUM"	"Find subcloning strategies"
"Mapmaker"	"Mapping with molecular and phenotypic markers"
"MCLAMP"	"Multiple alignment viewer"
"MWC"	"Oligonucleotide Molecular Weight Calculator"
"NCBI"	"Database tools - Natl. Ctr. for Biotech. Information"
"OGMP"	"Sequence retrieval"
"OSP"	"Oligonucleotide design"
"PHYLIP"	"Package for Inferring Phylogenies"
"PHYLO_WIN"	"Phylogenetic analysis"
"PRIMER3"	"Oligonucleotide design"
"READSEQ"	"Sequence format translator"
"TACG"	"Restriction digest analysis"
"TCOFFEE"	"Multiple sequence alignment"
"TREETOOL"	"Phylogenetic tree editor"
"XLANDSCAPE"	"Find motifs in a group of sequences"
"XYLEM"	"Create and manipulate database subsets"




 // Class Peptide 



 // Class DNA 



 // Class MatchTable 



 // Class Package 

Package : "ACeDB"
Description	 "Object-oriented biological database engine"
Category	 "Database"
Documentation	 "$doc\/acedb\/acedb-man-0.pdf"
Program	 "xace"
Program	 "tace"
Program	 "acedemo"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Package : "ARTEMIS"
Description	 "DNA sequence annotation"
Program	 "artemis"

Package : "CLUSTAL"
Description	 "Multiple sequence alignment"
Category	 "Sequence - Multiple Alignment"
Program	 "clustalw"
Program	 "clustalx"

Package : "CONSENSUS"
Description	 "Create consensus patterns from unaligned sequences"
Category	 "Sequence - Pattern Discovery and Matching"
Program	 "consensus"
Program	 "wconsensus"
Program	 "patser"
Program	 "gmat-inf-gc"

Package : "DNA-GUI"
Description	 "Gel image analysis and annotation"
Program	 "dui"

Package : "EBI"
Description	 "Sequence chromatogram viewer"
Program	 "TraceView"

Package : "FASTA"
Description	 "Pairwise and global similarity searches"
Program	 "fromgb"
Program	 "garnier"
Program	 "grease"
Program	 "align"
Program	 "bestscor"
Program	 "fasta"
Program	 "lalign"
Program	 "lfasta"
Program	 "tfasta"
Program	 "prdf"
Program	 "prss"
Program	 "relate"
Program	 "mrtrans"
Program	 "ssearch"
Program	 "fastx"
Program	 "fasty"
Program	 "randseq"

Package : "FASTDNAML"
Description	 "Maximum likelihood sequence phylogeny"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Program	 "fastDNAml"

Package : "forester"
Description	 "Programs and API for phylogeny"
Category	 "Phylogeny"
Documentation	 "$doc\/forester\/NHX.pdf"
Program	 "atv"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Package : "FSAP"
Description	 "Sequence analysis tools"
Category	 "Sequence"
Program	 "numseq"
Program	 "intrest"
Program	 "bachrest"
Program	 "funnel"
Program	 "digest"
Program	 "gel"
Program	 "prostat"
Program	 "p1hom"
Program	 "p2hom"
Program	 "d3hom"
Program	 "d4hom"
Program	 "testcode"
Platform	 "linux-intel"
Platform	 "solaris-sparc"
BIRCH	

Package : "GCUA"
Description	 "Codon usage analysis"
Category	 "Sequence - Annotation and Gene Discovery"
Program	 "gcua"

Package : "GDE"
Description	 "Genetic Data Environment"
Category	 "Sequence"
Category	 "Sequence - Multiple Alignment"
Program	 "gde"
Program	 "CAP2"

Package : "GENEPARSER"
Description	 "Parse a DNA sequence into introns and exons"
Program	 "gp"

Package : "ISREC"
Description	 "Multiple alignment display"
Program	 "boxshade"

Package : "LINDENBAUM"
Description	 "Find subcloning strategies"
Program	 "CloneIt"

Package : "Mapmaker"
Description	 "Mapping with molecular and phenotypic markers"
Category	 "Genetics"
Category	 "Molecular Markers"
Documentation	 "$doc\/mapmaker\/DataPreparationGuide.txt"
Program	 "Mapmaker"
Program	 "MapmakerQTL"
Platform	 "solaris-sparc"

Package : "MCLAMP"
Description	 "Multiple alignment viewer"
Program	 "Jalview"

Package : "MWC"
Description	 "Oligonucleotide Molecular Weight Calculator"
Program	 "MWCalculator"

Package : "NCBI"
Description	 "Database tools - Natl. Ctr. for Biotech. Information"
Program	 "sequin"
Program	 "Cn3D"
Program	 "entrez"
Program	 "blastcl3"

Package : "OGMP"
Description	 "Sequence retrieval"
Program	 "nclever"

Package : "OSP"
Description	 "Oligonucleotide design"
Category	 "Sequence - Oligonucleotides"
Program	 "osp"
Program	 "ospX"

Package : "PHYLIP"
Description	 "Package for Inferring Phylogenies"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Documentation	 "$doc\/Phylip\/main.html"
Documentation	 "$doc\/Phylip\/contchar.html"
Documentation	 "$doc\/Phylip\/discrete.html"
Documentation	 "$doc\/Phylip\/distance.html"
Documentation	 "$doc\/Phylip\/draw.html"
Documentation	 "$doc\/Phylip\/sequence.html"
Program	 "protpars"
Program	 "dnapars"
Program	 "dnamove"
Program	 "dnapenny"
Program	 "dnacomp"
Program	 "dnainvar"
Program	 "dnaml"
Program	 "dnamlk"
Program	 "dnadist"
Program	 "protdist"
Program	 "seqboot"
Program	 "fitch"
Program	 "kitsch"
Program	 "neighbor"
Program	 "contml"
Program	 "contrast"
Program	 "gendist"
Program	 "restml"
Program	 "restdist"
Program	 "mix"
Program	 "move"
Program	 "penny"
Program	 "dollop"
Program	 "dolmove"
Program	 "dolpenny"
Program	 "clique"
Program	 "factor"
Program	 "drawgram"
Program	 "drawtree"
Program	 "consense"
Program	 "pars"
Program	 "treedist"

Package : "PHYLO_WIN"
Description	 "Phylogenetic analysis"
Program	 "phylo_win"

Package : "PRIMER3"
Description	 "Oligonucleotide design"
Program	 "primer3"

Package : "READSEQ"
Description	 "Sequence format translator"
Program	 "readseq"

Package : "TACG"
Description	 "Restriction digest analysis"
Program	 "tacg"

Package : "TCOFFEE"
Description	 "Multiple sequence alignment"
Program	 "tcoffee"

Package : "TREETOOL"
Description	 "Phylogenetic tree editor"
Program	 "treetool"

Package : "XLANDSCAPE"
Description	 "Find motifs in a group of sequences"
Program	 "xland"

Package : "XYLEM"
Description	 "Create and manipulate database subsets"
Category	 "Database"
Program	 "getob"
Program	 "findkey"
Program	 "ribosome"
Program	 "prot2nuc"
Program	 "clu2ig"
Program	 "reform"
Program	 "xylem_identify"
Program	 "fetch"
Program	 "features"
Program	 "splitdb"
Program	 "getloc"
Program	 "shuffle"
Program	 "dbstat"
Platform	 "linux-intel"
Platform	 "solaris-sparc"



 // Class Category 

Category : "Database"
Package	 "XYLEM"
Package	 "ACeDB"
Program	 "getob"
Program	 "findkey"
Program	 "xylem_identify"
Program	 "entrez"
Program	 "nclever"
Program	 "fetch"
Program	 "ssearch"
Program	 "fasta"
Program	 "fastx"
Program	 "fasty"
Program	 "tfasta"
Program	 "features"
Program	 "splitdb"
Program	 "getloc"
Program	 "shuffle"
Program	 "randseq"
Program	 "dbstat"
Program	 "blastcl3"
Program	 "xace"
Program	 "tace"
Program	 "acedemo"

Category : "Sequence"
Package	 "FSAP"
Package	 "GDE"
Program	 "gde"
Program	 "ribosome"
Program	 "prot2nuc"

Category : "Sequence - Multiple Alignment"
Package	 "GDE"
Package	 "CLUSTAL"
Program	 "clustalw"
Program	 "clustalx"
Program	 "reform"
Program	 "Jalview"
Program	 "boxshade"
Program	 "clu2ig"
Program	 "mrtrans"
Program	 "tcoffee"
Program	 "gde"

Category : "Sequence - Annotation and Gene Discovery"
Package	 "GCUA"
Program	 "artemis"
Program	 "testcode"
Program	 "gcua"

Category : "Sequence - Oligonucleotides"
Package	 "OSP"
Program	 "primer3"
Program	 "osp"
Program	 "ospX"
Program	 "MWCalculator"

Category : "Sequence - Pattern Discovery and Matching"
Package	 "CONSENSUS"
Program	 "gp"
Program	 "xland"
Program	 "consensus"
Program	 "wconsensus"
Program	 "patser"
Program	 "gmat-inf-gc"

Category : "Phylogeny"
Package	 "PHYLIP"
Package	 "FASTDNAML"
Package	 "forester"
Program	 "treetool"
Program	 "phylo_win"
Program	 "protpars"
Program	 "dnapars"
Program	 "dnamove"
Program	 "dnapenny"
Program	 "dnacomp"
Program	 "dnainvar"
Program	 "dnaml"
Program	 "fastDNAml"
Program	 "dnamlk"
Program	 "dnadist"
Program	 "protdist"
Program	 "seqboot"
Program	 "fitch"
Program	 "kitsch"
Program	 "neighbor"
Program	 "contml"
Program	 "contrast"
Program	 "gendist"
Program	 "restml"
Program	 "restdist"
Program	 "mix"
Program	 "move"
Program	 "penny"
Program	 "dollop"
Program	 "dolmove"
Program	 "dolpenny"
Program	 "clique"
Program	 "factor"
Program	 "drawgram"
Program	 "drawtree"
Program	 "consense"
Program	 "atv"
Program	 "pars"
Program	 "treedist"

Category : "Sequence - Phylogeny"
Package	 "PHYLIP"
Package	 "FASTDNAML"
Program	 "treetool"
Program	 "phylo_win"
Program	 "protpars"
Program	 "dnapars"
Program	 "dnamove"
Program	 "dnapenny"
Program	 "dnacomp"
Program	 "dnainvar"
Program	 "dnaml"
Program	 "fastDNAml"
Program	 "dnamlk"
Program	 "dnadist"
Program	 "protdist"
Program	 "seqboot"
Program	 "fitch"
Program	 "kitsch"
Program	 "neighbor"
Program	 "dollop"
Program	 "drawgram"
Program	 "drawtree"
Program	 "consense"
Program	 "atv"
Program	 "treedist"

Category : "Genetics"
Package	 "Mapmaker"
Program	 "Mapmaker"
Program	 "MapmakerQTL"

Category : "Molecular Markers"
Package	 "Mapmaker"
Program	 "Mapmaker"
Program	 "MapmakerQTL"
Program	 "restml"
Program	 "restdist"
Program	 "fitch"
Program	 "kitsch"
Program	 "neighbor"
Program	 "mix"
Program	 "dollop"
Program	 "drawgram"
Program	 "drawtree"
Program	 "atv"
Program	 "treedist"
Program	 "treetool"

Category : "Gene Expression"

Category : "Sequence - Protein"
Program	 "prostat"
Program	 "garnier"
Program	 "grease"
Program	 "Cn3D"

Category : "Sequence - Protein Structure"
Program	 "Cn3D"

Category : "Sequence - Pairwise Similarity"
Program	 "p1hom"
Program	 "p2hom"
Program	 "d3hom"
Program	 "d4hom"
Program	 "align"
Program	 "bestscor"
Program	 "fasta"
Program	 "lalign"
Program	 "lfasta"
Program	 "tfasta"
Program	 "prdf"
Program	 "prss"
Program	 "relate"
Program	 "blastcl3"

Category : "BIRCH - Administration"

Category : "Sequence - DNA Sequencing"
Program	 "sequin"
Program	 "TraceView"
Program	 "CAP2"
Program	 "gde"
Program	 "artemis"

Category : "Sequence - File Formatting"
Program	 "readseq"
Program	 "fromgb"
Program	 "funnel"
Program	 "numseq"
Program	 "clu2ig"

Category : "Sequence - Restriction Analysis"
Program	 "intrest"
Program	 "bachrest"
Program	 "digest"
Program	 "gel"
Program	 "tacg"
Program	 "CloneIt"

Category : "Gel Electrophoresis"
Program	 "gel"
Program	 "dui"

Category : "Laboratory Information Management"

Category : "Sequence - RNA Structure"

Category : "Sequence - Database Search"

Category : "Programming Tools"

Category : "Utilities"



 // Class File 

File : "$doc\/Phylip\/main.html"
Description	 "Main Phylip documentation file"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/main.html"

File : "$doc\/Phylip\/contchar.html"
Description	 "Continuous character programs"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/contchar.html"

File : "$doc\/Phylip\/discrete.html"
Description	 "Discrete (0,1) character programs"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/discrete.html"

File : "$doc\/Phylip\/distance.html"
Description	 "Distance matrix programs"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/distance.html"

File : "$doc\/Phylip\/draw.html"
Description	 "Tree drawing programs"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/draw.html"

File : "$doc\/Phylip\/sequence.html"
Description	 "Sequence phylogeny programs"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/sequence.html"

File : "$doc\/forester\/NHX.pdf"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/forester\/NHX.pdf"

File : "$doc\/mapmaker\/DataPreparationGuide.txt"
Description	 "Data Preparation Guide"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/mapmaker\/DataPreparationGuide.txt"

File : "$doc\/acedb\/acedb-man-0.pdf"
Description	 "User's Guide"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/acedb\/acedb-man-0.pdf"

File : "$doc\/fsap\/numseq.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fsap\/numseq.asc"

File : "$doc\/GDE\/GDE2.2_manual.ps"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/GDE\/GDE2.2_manual.ps"

File : "$doc\/entrez\/sequin.htm"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/entrez\/sequin.htm"

File : "$doc\/EBI\/trace_viewer_paper.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/EBI\/trace_viewer_paper.html"

File : "$doc\/GDE\/CAP2.help"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/GDE\/CAP2.help"

File : "$doc\/fsap\/numseq.txt"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fsap\/numseq.txt"

File : "$doc\/xylem\/ribosome.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/ribosome.txt"

File : "$doc\/xylem\/prot2nuc.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/prot2nuc.txt"

File : "$doc\/readseq\/readseq.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/readseq\/readseq.asc"

File : "$doc\/readseq\/readseq-help.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/readseq\/readseq-help.html"

File : "$doc\/readseq\/Readseq2-help.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/readseq\/Readseq2-help.html"

File : "$doc\/fasta\/format.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fasta\/format.asc"

File : "$doc\/fsap\/funnel.as"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fsap\/funnel.as"

File : "$doc\/clustalw\/clu2ig.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/clu2ig.txt"

File : "$doc\/fsap\/rest.txt"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fsap\/rest.txt"

File : "$doc\/fsap\/digest.txt"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fsap\/digest.txt"

File : "$doc\/fsap\/gel.txt"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fsap\/gel.txt"

File : "$doc\/tacg\/tacg.main.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/tacg\/tacg.main.html"

File : "$doc\/cloneit.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/cloneit.html"

File : "$doc\/DNA-GUI\/dnagui_ug.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/DNA-GUI\/dnagui_ug.html"

File : "$doc\/DNA-GUI\/guide.ps"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/DNA-GUI\/guide.ps"

File : "$doc\/fsap\/prostat.txt"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fsap\/prostat.txt"

File : "$doc\/fasta\/fasta.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fasta\/fasta.asc"

File : "$doc\/fasta\/fasta.as"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fasta\/fasta.as"

File : "http:\/\/www.ncbi.nlm.nih.gov\/Structure\/CN3D\/cn3d.shtml"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "http:\/\/www.ncbi.nlm.nih.gov\/Structure\/CN3D\/cn3d.shtml"

File : "$doc\/fsap\/hom.txt"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fsap\/hom.txt"

File : "$doc\/fasta\/fasta20.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fasta\/fasta20.asc"

File : "$doc\/gcua\/codon.hlp"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/gcua\/codon.hlp"

File : "$doc\/fsap\/testcode.txt"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fsap\/testcode.asc"

File : "$doc\/clustalw\/clustalw.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/clustalw\/clustalw.asc"

File : "$doc\/clustalx\/clustalx.htm"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/clustalx\/clustalx.htm"

File : "$doc\/xylem\/reform.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/reform.asc"

File : "$doc\/jalview\/help.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/jalview\/help.html"

File : "$doc\/boxshade.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/boxshade.asc"

File : "$doc\/fasta\/mrtrans.txt"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fasta\/mrtrans.txt"

File : "$doc\/tcoffee\/t_coffee_doc.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/tcoffee\/t_coffee_doc.html"

File : "$doc\/tcoffee\/t_coffee_doc.pdf"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/tcoffee\/t_coffee_doc.pdf"

File : "$doc\/primer\/primer3.html"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/primer\/primer3.html"

File : "$doc\/primer\/primer3.ps"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/primer\/primer3.ps"

File : "$doc\/primer\/example"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/primer\/example"

File : "$doc\/osp\/INSTR.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/osp\/INSTR.asc"

File : "http:\/\/www-classes.cs.uchicago.edu\/~gluc\/MWC\/MWC.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "http:\/\/www-classes.cs.uchicago.edu\/~gluc\/MWC\/MWC.html"

File : "$doc\/xylem\/findkey.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/findkey.txt"

File : "$doc\/xylem\/identify.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/identify.asc"

File : "$doc\/entrez\/entrzdoc.txt"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/entrez\/entrzdoc.txt"

File : "$doc\/nclever\/nclever_manual.txt"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/nclever\/nclever_manual.txt"

File : "$doc\/xylem\/fetch.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/fetch.txt"

File : "$doc\/xylem\/features.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/features.txt"

File : "$doc\/xylem\/splitdb.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/splitdb.txt"

File : "$doc\/xylem\/getloc.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/getloc.txt"

File : "$doc\/xylem\/getob.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/getob.txt"

File : "$doc\/xylem\/shuffle.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/shuffle.txt"

File : "$doc\/xylem\/dbstat.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/xylem\/dbstat.txt"

File : "$doc\/geneparser\/GeneParser.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/geneparser\/GeneParser.asc"

File : "$doc\/XLandscape\/readme.txt"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/XLandscape\/readme.txt"

File : "$doc\/Consensus\/consensus.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Consensus\/consensus.asc"

File : "$doc\/Consensus\/wconsensus.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Consensus\/wconsensus.asc"

File : "$doc\/Consensus\/patser.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Consensus\/patser.asc"

File : "$doc\/Consensus\/gmat-inf-gc.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Consensus\/gmat-inf-gc.asc"

File : "$doc\/treetool.txt"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/treetool.txt"

File : "$doc\/Phylip\/fastDNAml\/fastDNAml_doc.txt"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/fastDNAml\/fastDNAml_doc.txt"

File : "http:\/\/pbil.univ-lyon1.fr\/software\/phylowin.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "http:\/\/pbil.univ-lyon1.fr\/software\/phylowin.html"

File : "http:\/\/www-igbmc.u-strasbg.fr\/BioInfo\/ClustalW\/"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "http:\/\/www-igbmc.u-strasbg.fr\/BioInfo\/ClustalW\/"

File : "$doc\/fasta\/fasta3x.asc"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fasta\/fasta3x.asc"

File : "http:\/\/www.people.virginia.edu\/~wrp\/"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "http:\/\/www.people.virginia.edu\/~wrp\/"

File : "http:\/\/evolution.genetics.washington.edu\/phylip.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "http:\/\/evolution.genetics.washington.edu\/phylip.html"

File : "$doc\/Phylip\/drawgram.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/drawgram.html"

File : "$dat\/REBASE\/type2.lst"
Description	 "REBASE TypeII restriction enzymes"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$dat\/REBASE\/type2.lst"

File : "$doc\/fsap\/funnel.txt"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fsap\/funnel.txt"

File : "$doc\/NCBI\/netblast\/netblast.txt"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/NCBI\/netblast\/netblast.txt"

File : "$doc\/Phylip\/clique.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/clique.html"

File : "$doc\/Phylip\/consense.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/consense.html"

File : "$doc\/Phylip\/contml.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/contml.html"

File : "$doc\/Phylip\/contrast.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/contrast.html"

File : "$doc\/Phylip\/dnacomp.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dnacomp.html"

File : "$doc\/Phylip\/dnadist.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dnadist.html"

File : "$doc\/Phylip\/dnainvar.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dnainvar.html"

File : "$doc\/Phylip\/dnaml.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dnaml.html"

File : "$doc\/Phylip\/dnamlk.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dnamlk.html"

File : "$doc\/Phylip\/dnamove.html"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dnamove.html"

File : "$doc\/Phylip\/dnapars.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dnapars.html"

File : "$doc\/Phylip\/dnapenny.html"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dnapenny.html"

File : "$doc\/Phylip\/dolboot.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dolboot.html"

File : "$doc\/Phylip\/dollop.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dollop.html"

File : "$doc\/Phylip\/dolmove.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dolmove.html"

File : "$doc\/Phylip\/dolpenny.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/dolpenny.html"

File : "$doc\/Phylip\/drawtree.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/drawtree.html"

File : "$doc\/Phylip\/factor.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/factor.html"

File : "$doc\/Phylip\/fitch.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/fitch.html"

File : "$doc\/Phylip\/gendist.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/gendist.html"

File : "$doc\/Phylip\/kitsch.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/kitsch.html"

File : "$doc\/Phylip\/mix.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/mix.html"

File : "$doc\/Phylip\/move.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/move.html"

File : "$doc\/Phylip\/neighbor.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/neighbor.html"

File : "$doc\/Phylip\/penny.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/penny.html"

File : "$doc\/Phylip\/protdist.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/protdist.html"

File : "$doc\/Phylip\/protpars.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/protpars.html"

File : "$doc\/Phylip\/restdist.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/restdist.html"

File : "$doc\/Phylip\/restml.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/restml.html"

File : "$doc\/Phylip\/seqboot.html"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/seqboot.html"

File : "$doc\/forester\/atv_documentation.pdf"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/forester\/atv_documentation.pdf"

File : "$doc\/mapmaker\/mapmaker.refguide.pdf"
Description	 "User's Guide"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/mapmaker\/mapmaker.refguide.pdf"

File : "$doc\/mapmaker\/mapmaker.tutorial.pdf"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/mapmaker\/mapmaker.tutorial.pdf"

File : "$doc\/mapmaker\/mapmakerQTL.tutorial.pdf"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/mapmaker\/mapmakerQTL.tutorial.pdf"

File : "$doc\/mapmaker\/mapmakerqtl.refguide.pdf"
Description	 "User's Guide"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/mapmaker\/mapmakerqtl.refguide.pdf"

File : "$doc\/mapmaker\/mapmaker.refguide.ps"
Description	 "User's Guide"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/mapmaker\/mapmaker.refguide.ps"

File : "$doc\/mapmaker\/mapmaker.tutorial.ps"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/mapmaker\/mapmaker.tutorial.ps"

File : "$doc\/mapmaker\/mapmakerQTL.tutorial.ps"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/mapmaker\/mapmakerQTL.tutorial.ps"

File : "$doc\/mapmaker\/mapmakerqtl.refguide.ps"
Description	 "User's Guide"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/mapmaker\/mapmakerqtl.refguide.ps"

File : "$dat\/mapmaker\/mouse.in"
Description	 "Tutorial commands for mouse data"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$dat\/mapmaker\/mouse.in"

File : "$dat\/mapmaker\/mouse.prep"
Description	 "Initilization file for mouse data"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$dat\/mapmaker\/mouse.prep"

File : "$dat\/mapmaker\/mouse.raw"
Description	 "Mouse F2 - 308 markers, 46 progeny"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$dat\/mapmaker\/mouse.raw"

File : "$dat\/mapmaker\/sample.in"
Description	 "Tutorial commands from sample data"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$dat\/mapmaker\/sample.in"

File : "$dat\/mapmaker\/sample.inp"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$dat\/mapmaker\/sample.inp"

File : "$dat\/mapmaker\/sample.inq"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$dat\/mapmaker\/sample.inq"

File : "$dat\/mapmaker\/sample.raw"
Description	 "Sample F2 data"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$dat\/mapmaker\/sample.raw"

File : "$tutorials\/GDE\/sequence\/sequence.html"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$tutorials\/GDE\/sequence\/sequence.html"

File : "$tutorials\/GDE\/dotmatrix\/dotmatrix.html"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$tutorials\/GDE\/dotmatrix\/dotmatrix.html"

File : "$doc\/artemis\/manual\/index.shtml"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/artemis\/manual\/index.shtml"

File : "$tutorials\/GDE\/keywords\/keywords.html"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$tutorials\/GDE\/keywords\/keywords.html"

File : "$tutorials\/GDE\/dataset\/dataset.html"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$tutorials\/GDE\/dataset\/dataset.html"

File : "$tutorials\/GDE\/database.sim\/database.sim.html"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$tutorials\/GDE\/database.sim\/database.sim.html"

File : "$tutorials\/GDE\/discrete\/discrete.html"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$tutorials\/GDE\/discrete\/discrete.html"

File : "$tutorials\/GDE\/multalign\/multalign.html"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$tutorials\/GDE\/multalign\/multalign.html"

File : "$tutorials\/GDE\/pairwise.sim\/pairwise.sim.html"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$tutorials\/GDE\/pairwise.sim\/pairwise.sim.html"

File : "$doc\/Phylip\/retree.html"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/retree.html"

File : "$doc\/Phylip\/treedist.html"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/treedist.html"

File : "$doc\/Phylip\/pars.html"
Description	 "Documentation"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/Phylip\/pars.html"

File : "$doc\/fasta\/prss.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fasta\/prss.txt"

File : "$doc\/fasta\/prdf.txt"
Description	 "Manual"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/fasta\/prdf.txt"



 // Class Program 

Program : "getob"
Description	 "Parse features from GenBank flatfiles"
Category	 "Database"
command	 "getob [-frcn] infile namefile anofile seqfile indfile message [outfile] expressionfile"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/getob.txt"
Platform	 "linux-intel"
Platform	 "solaris-sparc"
BIRCH	

Program : "findkey"
Description	 "Keyword search on local flatfile database"
Category	 "Database"
command	 "findkey [options] keywordfile [namefile findfile]"
interactive	 "findkey"
GDE	 "Database --> FINDKEY"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/findkey.txt"
Documentation	 "$tutorials\/GDE\/keywords\/keywords.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "ribosome"
Description	 "Translate nucleic acid to protein"
Category	 "Sequence"
command	 "ribosome [-g gcfile]"
GDE	 "DNA\/RNA --> Ribosome"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/ribosome.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "prot2nuc"
Description	 "Reverse translate protein to degenerate DNA"
Category	 "Sequence"
command	 "prot2nuc [-ln -gn]"
GDE	 "Protein --> PROT2NUC"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/prot2nuc.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "clu2ig"
Description	 "Translate multiply aligned sequences in clustal format to Intelligenetics format"
Category	 "Sequence - Multiple Alignment"
Category	 "Sequence - File Formatting"
command	 "clu2ig clustalfile"
Package	 "XYLEM"
Documentation	 "$doc\/clustalw\/clu2ig.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "reform"
Description	 "print a multiple alignment using plain text"
Category	 "Sequence - Multiple Alignment"
command	 "reform [-gpcnm] [-fx] [-sn] [-ln] "
GDE	 "Alignment --> REFORM"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/reform.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "xylem_identify"
Description	 "used by FINDKEY to extract LOCUS names from database hits"
Category	 "Database"
command	 "xylem_identify grepfile indfile namefile findfile"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/identify.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "fetch"
Description	 "retrieve entries from local flatfile database by name or accession number"
Category	 "Database"
command	 "fetch [options] namefile [outputfile]"
interactive	 "fetch"
GDE	 "Database --> FETCH"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/fetch.txt"
Documentation	 "$tutorials\/GDE\/keywords\/keywords.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "features"
Description	 "extract features from GenBank flatfile entries"
Category	 "Database"
command	 "features expression"
command	 "features [-f featurekey | -F keyfile] [-n name | -a accession | -e expression | -N namefile | -A accessionfile | -E expfile] [-u dbfile | -U dbfile | -g ]"
interactive	 "features"
GDE	 "Database --> FEATURES"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/features.txt"
Documentation	 "$tutorials\/GDE\/dataset\/dataset.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "splitdb"
Description	 "split a GenBank flatfile into a database containing annotation, sequence and index"
Category	 "Database"
command	 "splitdb [-gepvlct] genbankfile anofile seqfile indfile"
GDE	 "File --> SPLITDB"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/splitdb.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "getloc"
Description	 "retrieve entries from a local flatfile database"
Category	 "Database"
command	 "getloc [asfcgepvl] namefile [anofile] [seqfile] indfile outfile"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/getloc.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "shuffle"
Description	 "randomize sequences using a sliding window"
Category	 "Database"
command	 "shuffle -sn [-wn -on]"
GDE	 "Similarity --> SHUFFLE"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/shuffle.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "dbstat"
Description	 "Calculates amino acid frequencies for one or more proteins"
Category	 "Database"
command	 "dbstat"
GDE	 "Protein --> Protein statistics"
Package	 "XYLEM"
Documentation	 "$doc\/xylem\/dbstat.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "numseq"
Description	 "Sequence dislpay and manipulation"
Category	 "Sequence - File Formatting"
interactive	 "numseq"
GDE	 "DNA\/RNA --> NUMSEQ"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/numseq.txt"
Documentation	 "$tutorials\/GDE\/sequence\/sequence.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "intrest"
Description	 "Restriction site search"
Category	 "Sequence - Restriction Analysis"
interactive	 "intrest"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/rest.txt"
Data	
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "bachrest"
Category	 "Sequence - Restriction Analysis"
interactive	 "bachrest"
GDE	 "DNA\/RNA --> BACHREST"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/rest.txt"
Documentation	 "$tutorials\/GDE\/sequence\/sequence.html"
Data	 "$dat\/REBASE\/type2.lst"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "funnel"
Description	 "Reformats a free-format or FASTA-format file to a fixed line-length, preserving comments that begin with a semicolon (\;)"
Category	 "Sequence - File Formatting"
interactive	 "funnel"
GDE	 "File --> Import Free Format"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/funnel.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "digest"
Description	 "Calculates restriction sites, fragments and fragment ends for multiple enzyme digests, complete or partial"
Category	 "Sequence - Restriction Analysis"
interactive	 "digest"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/digest.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "gel"
Description	 "Given migration distances for standards of know size, calculate sizes of unknown fragments"
Category	 "Sequence - Restriction Analysis"
Category	 "Gel Electrophoresis"
interactive	 "gel"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/gel.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "prostat"
Description	 "Calculates amino acid frequencies for one or more proteins"
Category	 "Sequence - Protein"
interactive	 "prostat"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/prostat.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "p1hom"
Description	 "Dot-matrix protein similarity, k=1"
Category	 "Sequence - Pairwise Similarity"
interactive	 "p1hom"
GDE	 "Similarity --> PXHOM"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/hom.txt"
Documentation	 "$tutorials\/GDE\/dotmatrix\/dotmatrix.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "p2hom"
Description	 "Dot-matrix protein similarity, k=2"
Category	 "Sequence - Pairwise Similarity"
interactive	 "p2hom"
GDE	 "Similarity --> PXHOM"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/hom.txt"
Documentation	 "$tutorials\/GDE\/dotmatrix\/dotmatrix.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "d3hom"
Description	 "Dot-matrix DNA similarity, k=3"
Category	 "Sequence - Pairwise Similarity"
interactive	 "d3hom"
GDE	 "Similarity --> DXHOM"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/hom.txt"
Documentation	 "$tutorials\/GDE\/dotmatrix\/dotmatrix.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "d4hom"
Description	 "Dot-matrix DNA similarity, k=4"
Category	 "Sequence - Pairwise Similarity"
interactive	 "d4hom"
GDE	 "Similarity --> DXHOM"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/hom.txt"
Documentation	 "$tutorials\/GDE\/dotmatrix\/dotmatrix.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "testcode"
Description	 "Find protein coding regions using method of Fickett"
Category	 "Sequence - Annotation and Gene Discovery"
interactive	 "testcode"
GDE	 "Patterns --> Testcode"
Package	 "FSAP"
Documentation	 "$doc\/fsap\/testcode.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "gde"
Description	 "Genetic Data Environment"
Category	 "Sequence"
Category	 "Sequence - Multiple Alignment"
Category	 "Sequence - DNA Sequencing"
gui	 "gde [filename]"
GDE	
Package	 "GDE"
Documentation	 "$doc\/GDE\/GDE2.2_manual.ps"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "CAP2"
Category	 "Sequence - DNA Sequencing"
command	 "CAP2 [options]"
Package	 "GDE"
Documentation	 "$doc\/GDE\/CAP2.help"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "sequin"
Description	 "Annotate and submit sequences to GenBank"
Category	 "Sequence - DNA Sequencing"
gui	 "sequin"
Package	 "NCBI"
Documentation	 "$doc\/entrez\/sequin.htm"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "Cn3D"
Description	 "Protein 3D structure viewer"
Category	 "Sequence - Protein"
Category	 "Sequence - Protein Structure"
gui	 "Cn3D"
Package	 "NCBI"
Documentation	 "http:\/\/www.ncbi.nlm.nih.gov\/Structure\/CN3D\/cn3d.shtml"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "entrez"
Description	 "Find and Retrieve Data from NCBI"
Category	 "Database"
gui	 "entrez"
Package	 "NCBI"
Documentation	 "$doc\/entrez\/entrzdoc.txt"
Documentation	 "$tutorials\/GDE\/dataset\/dataset.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "blastcl3"
Description	 "run BLAST remotely at NCBI"
Category	 "Database"
Category	 "Sequence - Pairwise Similarity"
command	 "blastcl3 [options]"
GDE	 "Database --> BLAST*"
Package	 "NCBI"
Documentation	 "$doc\/NCBI\/netblast\/netblast.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "TraceView"
Description	 "Sequence chromatogram viewer"
Category	 "Sequence - DNA Sequencing"
command	 "TraceView [options]"
Package	 "EBI"
Documentation	 "$doc\/EBI\/trace_viewer_paper.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "readseq"
Category	 "Sequence - File Formatting"
command	 "readseq [options]"
interactive	 "readseq"
Package	 "READSEQ"
Documentation	 "$doc\/readseq\/readseq.asc"
Documentation	 "$doc\/readseq\/readseq-help.html"
Documentation	 "$doc\/readseq\/Readseq2-help.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "fromgb"
Category	 "Sequence - File Formatting"
interactive	 "fromgb"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/format.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "garnier"
Category	 "Sequence - Protein"
interactive	 "garnier"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "grease"
Category	 "Sequence - Protein"
interactive	 "grease"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta.as"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "align"
Category	 "Sequence - Pairwise Similarity"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta20.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "bestscor"
Category	 "Sequence - Pairwise Similarity"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta20.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "fasta"
Category	 "Database"
Category	 "Sequence - Pairwise Similarity"
command	 "fasta3 [options]"
interactive	 "fasta3"
GDE	 "Database --> fasta"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta20.asc"
Documentation	 "$doc\/fasta\/fasta.asc"
Documentation	 "$tutorials\/GDE\/database.sim\/database.sim.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "lalign"
Category	 "Sequence - Pairwise Similarity"
command	 "lalign [options]"
interactive	 "lalign"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta20.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "lfasta"
Category	 "Sequence - Pairwise Similarity"
command	 "lfasta [options]"
interactive	 "lfasta"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta20.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "tfasta"
Category	 "Database"
Category	 "Sequence - Pairwise Similarity"
command	 "tfasta [options]"
interactive	 "tfasta"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta20.asc"
Documentation	 "$doc\/fasta\/fasta.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "prdf"
Description	 "Statistical significance of pairwise similarities"
Category	 "Sequence - Pairwise Similarity"
command	 "prdf [options]"
interactive	 "prdf"
GDE	 "Similarity --> PRDF"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta20.asc"
Documentation	 "$tutorials\/GDE\/pairwise.sim\/pairwise.sim.html"
Documentation	 "$doc\/fasta\/prdf.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "prss"
Description	 "Statistical significance of pairwise similarities"
Category	 "Sequence - Pairwise Similarity"
command	 "prss [options]"
interactive	 "prss"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta20.asc"
Documentation	 "$tutorials\/GDE\/pairwise.sim\/pairwise.sim.html"
Documentation	 "$doc\/fasta\/prss.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "relate"
Category	 "Sequence - Pairwise Similarity"
interactive	 "relate"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta20.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "mrtrans"
Category	 "Sequence - Multiple Alignment"
command	 "mrtrans [options]"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/mrtrans.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "ssearch"
Category	 "Database"
command	 "ssearch [options]"
interactive	 "ssearch"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "fastx"
Category	 "Database"
command	 "fastx [options]"
interactive	 "fastx"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "fasty"
Category	 "Database"
command	 "fasty [options]"
interactive	 "fasty"
Package	 "FASTA"
Documentation	 "$doc\/fasta\/fasta.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "randseq"
Category	 "Database"
command	 "randseq [options]"
Package	 "FASTA"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "tacg"
Category	 "Sequence - Restriction Analysis"
command	 "tacg [options]"
Package	 "TACG"
Documentation	 "$doc\/tacg\/tacg.main.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "CloneIt"
Description	 "Find subcloning strategies"
Category	 "Sequence - Restriction Analysis"
command	 "CloneIt [options]"
interactive	 "CloneIt"
Package	 "LINDENBAUM"
Documentation	 "$doc\/cloneit.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "dui"
Description	 "Gel image analysis and annotation"
Category	 "Gel Electrophoresis"
interactive	 "dui"
Package	 "DNA-GUI"
Documentation	 "$doc\/DNA-GUI\/dnagui_ug.html"
Documentation	 "$doc\/DNA-GUI\/guide.ps"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "gcua"
Category	 "Sequence - Annotation and Gene Discovery"
interactive	 "gcua"
Package	 "GCUA"
Documentation	 "$doc\/gcua\/codon.hlp"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "clustalw"
Category	 "Sequence - Multiple Alignment"
interactive	 "clustalw"
Package	 "CLUSTAL"
Documentation	 "$doc\/clustalw\/clustalw.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "clustalx"
Category	 "Sequence - Multiple Alignment"
interactive	 "clustalx"
Package	 "CLUSTAL"
Documentation	 "$doc\/clustalx\/clustalx.htm"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "Jalview"
Description	 "Multiple alignment viewer"
Category	 "Sequence - Multiple Alignment"
command	 "Jalview [filename]"
GDE	 "Alignment --> Jalview"
Package	 "MCLAMP"
Documentation	 "$doc\/jalview\/help.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "boxshade"
Description	 "Multiple alignment display"
Category	 "Sequence - Multiple Alignment"
command	 "boxshade [options]"
interactive	 "boxshade"
GDE	 "Alignment --> Boxshade"
Package	 "ISREC"
Documentation	 "$doc\/boxshade.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "tcoffee"
Category	 "Sequence - Multiple Alignment"
command	 "tcoffee [options]"
Package	 "TCOFFEE"
Documentation	 "$doc\/tcoffee\/t_coffee_doc.html"
Documentation	 "$doc\/tcoffee\/t_coffee_doc.pdf"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "primer3"
Category	 "Sequence - Oligonucleotides"
command	 "primer3 [options]"
interactive	 "primer3"
Package	 "PRIMER3"
Documentation	 "$doc\/primer\/primer3.html"
Documentation	 "$doc\/primer\/primer3.ps"
Sample_input	 "$doc\/primer\/example"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "osp"
Category	 "Sequence - Oligonucleotides"
interactive	 "osp"
Package	 "OSP"
Documentation	 "$doc\/osp\/INSTR.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "ospX"
Category	 "Sequence - Oligonucleotides"
gui	 "ospX [filename]"
Package	 "OSP"
Documentation	 "$doc\/osp\/INSTR.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "MWCalculator"
Description	 "Calculate molecular weights for oligonucleotides"
Category	 "Sequence - Oligonucleotides"
Package	 "MWC"
Documentation	 "http:\/\/www-classes.cs.uchicago.edu\/~gluc\/MWC\/MWC.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "nclever"
Category	 "Database"
command	 "nclever [options]"
Package	 "OGMP"
Documentation	 "$doc\/nclever\/nclever_manual.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "gp"
Description	 "Parse a DNA sequence into introns and exons"
Category	 "Sequence - Pattern Discovery and Matching"
command	 "gp [options]"
Package	 "GENEPARSER"
Documentation	 "$doc\/geneparser\/GeneParser.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "xland"
Category	 "Sequence - Pattern Discovery and Matching"
command	 "xland [options]"
Package	 "XLANDSCAPE"
Documentation	 "$doc\/XLandscape\/readme.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "consensus"
Category	 "Sequence - Pattern Discovery and Matching"
command	 "consensus [options]"
Package	 "CONSENSUS"
Documentation	 "$doc\/Consensus\/consensus.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "wconsensus"
Category	 "Sequence - Pattern Discovery and Matching"
command	 "wconsensus [options]"
Package	 "CONSENSUS"
Documentation	 "$doc\/Consensus\/wconsensus.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "patser"
Category	 "Sequence - Pattern Discovery and Matching"
command	 "patser [options]"
Package	 "CONSENSUS"
Documentation	 "$doc\/Consensus\/patser.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "gmat-inf-gc"
Category	 "Sequence - Pattern Discovery and Matching"
command	 "gmat-inf-gc [options]"
Package	 "CONSENSUS"
Documentation	 "$doc\/Consensus\/gmat-inf-gc.asc"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "treetool"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Category	 "Molecular Markers"
Package	 "TREETOOL"
Documentation	 "$doc\/treetool.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "phylo_win"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
gui	 "phylo_win [filename]"
Package	 "PHYLO_WIN"
Documentation	 "http:\/\/pbil.univ-lyon1.fr\/software\/phylowin.html"
Platform	 "solaris-sparc"

Program : "protpars"
Description	 "Protein parsimony"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "protpars"
GDE	 "Phylogeny --> PROTPARS"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/protpars.html"
Documentation	 "$doc\/Phylip\/sequence.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "dnapars"
Description	 "DNA parsimony"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "dnapars"
GDE	 "Phylogeny --> DNAPARS"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/dnapars.html"
Documentation	 "$doc\/Phylip\/sequence.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "dnamove"
Description	 "DNA parsimony with interactive tree rearrangement"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "dnamove"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/dnamove.html"
Documentation	 "$doc\/Phylip\/sequence.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "dnapenny"
Description	 "DNA parsimony using branch and bound method"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "dnapenny"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/dnapenny.html"
Documentation	 "$doc\/Phylip\/sequence.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "dnacomp"
Description	 "DNA phylogeny using compatability method"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "dnacomp"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/dnacomp.html"
Documentation	 "$doc\/Phylip\/sequence.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "dnainvar"
Description	 "DNA sequence phylogeny invariants"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "dnainvar"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/dnainvar.html"
Documentation	 "$doc\/Phylip\/sequence.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "dnaml"
Description	 "DNA phylogeny using Maximum Likelihood"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "dnaml"
GDE	 "Phylogeny --> DNAML"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/dnaml.html"
Documentation	 "$doc\/Phylip\/sequence.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "dnamlk"
Description	 "DNA phylogeny using Maximum Likelihood (with evolutionary clock)"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "dnamlk"
GDE	 "Phylogeny --> DNAML"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/dnamlk.html"
Documentation	 "$doc\/Phylip\/sequence.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "dnadist"
Description	 "Construct distance matrix for DNA sequences"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "dnadist"
GDE	 "Phylogeny --> DNA Distance Methods"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/dnadist.html"
Documentation	 "$doc\/Phylip\/distance.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "protdist"
Description	 "Construct distance matrix for protein sequences"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "protdist"
GDE	 "Phylogeny --> Protein Distance Methods"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/protdist.html"
Documentation	 "$doc\/Phylip\/distance.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "seqboot"
Description	 "Create resampled datasets"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "seqboot"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/seqboot.html"
Documentation	 "$doc\/Phylip\/sequence.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "fitch"
Description	 "Distance trees - Fitch\/ Margoliash"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Category	 "Molecular Markers"
interactive	 "fitch"
GDE	 "Phylogeny --> DNA Distance Methods"
GDE	 "Phylogeny --> Protein Distance Methods"
GDE	 "Phylogeny --> Discrete Data Distance Methods"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/fitch.html"
Documentation	 "$doc\/Phylip\/distance.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "kitsch"
Description	 "Distance trees - Fitch\/ Margoliash (molecular clock)"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Category	 "Molecular Markers"
interactive	 "kitsch"
GDE	 "Phylogeny --> DNA Distance Methods"
GDE	 "Phylogeny --> Protein Distance Methods"
GDE	 "Phylogeny --> Discrete Data Distance Methods"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/kitsch.html"
Documentation	 "$doc\/Phylip\/distance.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "neighbor"
Description	 "Distance trees - Neighbor-Joining\/UPGMA"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Category	 "Molecular Markers"
interactive	 "neighbor"
GDE	 "Phylogeny --> DNA Distance Methods"
GDE	 "Phylogeny --> Protein Distance Methods"
GDE	 "Phylogeny --> Discrete Data Distance Methods"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/neighbor.html"
Documentation	 "$doc\/Phylip\/distance.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "contml"
Category	 "Phylogeny"
interactive	 "contml"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/contml.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "contrast"
Category	 "Phylogeny"
interactive	 "contrast"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/contrast.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "gendist"
Category	 "Phylogeny"
interactive	 "gendist"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/gendist.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "restml"
Category	 "Phylogeny"
Category	 "Molecular Markers"
interactive	 "restml"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/restml.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "restdist"
Category	 "Phylogeny"
Category	 "Molecular Markers"
interactive	 "restdist"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/restdist.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "mix"
Category	 "Phylogeny"
Category	 "Molecular Markers"
interactive	 "mix"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/mix.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "move"
Category	 "Phylogeny"
interactive	 "move"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/move.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "penny"
Category	 "Phylogeny"
interactive	 "penny"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/penny.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "dollop"
Description	 "Discrete data parsimony method of DOLLO"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Category	 "Molecular Markers"
interactive	 "dollop"
GDE	 "Phylogeny --> Discrete data parsimony"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/dollop.html"
Documentation	 "$doc\/Phylip\/discrete.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "dolmove"
Category	 "Phylogeny"
interactive	 "dolmove"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/dolmove.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "dolpenny"
Category	 "Phylogeny"
interactive	 "dolpenny"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/dolpenny.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "clique"
Category	 "Phylogeny"
interactive	 "clique"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/clique.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "factor"
Category	 "Phylogeny"
interactive	 "factor"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/factor.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "drawgram"
Description	 "Draw cladograms"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Category	 "Molecular Markers"
interactive	 "drawgram"
GDE	 "Phylogeny --> Drawgram"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/drawgram.html"
Documentation	 "$doc\/Phylip\/draw.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "drawtree"
Description	 "Draw radial trees"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Category	 "Molecular Markers"
interactive	 "drawtree"
GDE	 "Phylogeny --> Drawtree"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/drawtree.html"
Documentation	 "$doc\/Phylip\/draw.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "consense"
Description	 "Consensus trees"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
interactive	 "consense"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/consense.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "pars"
Description	 "Discrete character parsimony"
Category	 "Phylogeny"
interactive	 "pars"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/pars.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "treedist"
Description	 "Calculate distance between trees"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Category	 "Molecular Markers"
interactive	 "treedist"
Package	 "PHYLIP"
Documentation	 "$doc\/Phylip\/treedist.html"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "fastDNAml"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
command	 "fastDNAml [options]"
Package	 "FASTDNAML"
Documentation	 "$doc\/Phylip\/fastDNAml\/fastDNAml_doc.txt"
Platform	 "solaris-sparc"
Platform	 "linux-intel"

Program : "atv"
Description	 "Draw and edit phylogenetic trees"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Category	 "Molecular Markers"
gui	 "atv [filename]"
Package	 "forester"
Documentation	 "$doc\/forester\/atv_documentation.pdf"
Documentation	 "$doc\/forester\/NHX.pdf"

Program : "Mapmaker"
Description	 "Create genetic maps using marker and phenotype data"
Category	 "Genetics"
Category	 "Molecular Markers"
interactive	 "mapmaker"
Package	 "Mapmaker"
Documentation	 "$doc\/mapmaker\/mapmaker.refguide.pdf"
Documentation	 "$doc\/mapmaker\/mapmaker.refguide.ps"
Documentation	 "$doc\/mapmaker\/mapmaker.tutorial.pdf"
Documentation	 "$doc\/mapmaker\/mapmaker.tutorial.ps"
Documentation	 "$doc\/mapmaker\/DataPreparationGuide.txt"
Sample_input	 "$dat\/mapmaker\/sample.raw"
Sample_input	 "$dat\/mapmaker\/sample.in"
Sample_input	 "$dat\/mapmaker\/mouse.raw"
Sample_input	 "$dat\/mapmaker\/mouse.in"
Sample_input	 "$dat\/mapmaker\/mouse.prep"
Platform	 "solaris-sparc"

Program : "MapmakerQTL"
Description	 "Create maps for QTL data"
Category	 "Genetics"
Category	 "Molecular Markers"
interactive	 "qtl"
Package	 "Mapmaker"
Documentation	 "$doc\/mapmaker\/mapmakerqtl.refguide.pdf"
Documentation	 "$doc\/mapmaker\/mapmakerqtl.refguide.ps"
Documentation	 "$doc\/mapmaker\/mapmakerQTL.tutorial.pdf"
Documentation	 "$doc\/mapmaker\/mapmakerQTL.tutorial.ps"
Platform	 "solaris-sparc"

Program : "artemis"
Description	 "DNA sequence annotation tool"
Category	 "Sequence - DNA Sequencing"
Category	 "Sequence - Annotation and Gene Discovery"
gui	 "artemis [-quiet -fast] [-options optionsfile] [sequencefile]"
Package	 "ARTEMIS"
Documentation	 "$doc\/artemis\/manual\/index.shtml"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "xace"
Description	 "Graphic interface to ACeDB"
Category	 "Database"
gui	 "xace"
Package	 "ACeDB"
Documentation	 "$doc\/acedb\/acedb-man-0.pdf"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "tace"
Description	 "text interface to ACeDB"
Category	 "Database"
interactive	 "tace"
Package	 "ACeDB"
Documentation	 "$doc\/acedb\/acedb-man-0.pdf"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	

Program : "acedemo"
Description	 "Demonstration laboratory database"
Category	 "Database"
gui	 "acedemo"
Package	 "ACeDB"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
BIRCH	



 // Class Platform 

Platform : "linux-intel"
Package	 "XYLEM"
Package	 "FSAP"
Package	 "forester"
Package	 "ACeDB"
Program	 "getob"
Program	 "findkey"
Program	 "numseq"
Program	 "intrest"
Program	 "bachrest"
Program	 "gde"
Program	 "sequin"
Program	 "TraceView"
Program	 "CAP2"
Program	 "ribosome"
Program	 "prot2nuc"
Program	 "readseq"
Program	 "fromgb"
Program	 "funnel"
Program	 "clu2ig"
Program	 "digest"
Program	 "gel"
Program	 "tacg"
Program	 "CloneIt"
Program	 "dui"
Program	 "prostat"
Program	 "garnier"
Program	 "grease"
Program	 "Cn3D"
Program	 "p1hom"
Program	 "p2hom"
Program	 "d3hom"
Program	 "d4hom"
Program	 "align"
Program	 "bestscor"
Program	 "fasta"
Program	 "lalign"
Program	 "lfasta"
Program	 "tfasta"
Program	 "prdf"
Program	 "prss"
Program	 "relate"
Program	 "gcua"
Program	 "testcode"
Program	 "clustalw"
Program	 "clustalx"
Program	 "reform"
Program	 "Jalview"
Program	 "boxshade"
Program	 "mrtrans"
Program	 "tcoffee"
Program	 "primer3"
Program	 "osp"
Program	 "ospX"
Program	 "MWCalculator"
Program	 "xylem_identify"
Program	 "entrez"
Program	 "nclever"
Program	 "fetch"
Program	 "ssearch"
Program	 "fastx"
Program	 "fasty"
Program	 "features"
Program	 "splitdb"
Program	 "getloc"
Program	 "shuffle"
Program	 "randseq"
Program	 "dbstat"
Program	 "gp"
Program	 "xland"
Program	 "consensus"
Program	 "wconsensus"
Program	 "patser"
Program	 "gmat-inf-gc"
Program	 "treetool"
Program	 "protpars"
Program	 "dnapars"
Program	 "dnamove"
Program	 "dnapenny"
Program	 "dnacomp"
Program	 "dnainvar"
Program	 "dnaml"
Program	 "fastDNAml"
Program	 "dnamlk"
Program	 "dnadist"
Program	 "protdist"
Program	 "seqboot"
Program	 "fitch"
Program	 "kitsch"
Program	 "neighbor"
Program	 "contml"
Program	 "contrast"
Program	 "gendist"
Program	 "restml"
Program	 "restdist"
Program	 "mix"
Program	 "move"
Program	 "penny"
Program	 "dollop"
Program	 "dolmove"
Program	 "dolpenny"
Program	 "clique"
Program	 "factor"
Program	 "drawgram"
Program	 "drawtree"
Program	 "consense"
Program	 "blastcl3"
Program	 "artemis"
Program	 "xace"
Program	 "tace"
Program	 "pars"
Program	 "treedist"
Program	 "acedemo"

Platform : "solaris-sparc"
Package	 "XYLEM"
Package	 "FSAP"
Package	 "forester"
Package	 "Mapmaker"
Package	 "ACeDB"
Program	 "getob"
Program	 "findkey"
Program	 "numseq"
Program	 "intrest"
Program	 "bachrest"
Program	 "gde"
Program	 "sequin"
Program	 "TraceView"
Program	 "CAP2"
Program	 "ribosome"
Program	 "prot2nuc"
Program	 "readseq"
Program	 "fromgb"
Program	 "funnel"
Program	 "clu2ig"
Program	 "digest"
Program	 "gel"
Program	 "tacg"
Program	 "CloneIt"
Program	 "dui"
Program	 "prostat"
Program	 "garnier"
Program	 "grease"
Program	 "Cn3D"
Program	 "p1hom"
Program	 "p2hom"
Program	 "d3hom"
Program	 "d4hom"
Program	 "align"
Program	 "bestscor"
Program	 "fasta"
Program	 "lalign"
Program	 "lfasta"
Program	 "tfasta"
Program	 "prdf"
Program	 "prss"
Program	 "relate"
Program	 "gcua"
Program	 "testcode"
Program	 "clustalw"
Program	 "clustalx"
Program	 "reform"
Program	 "Jalview"
Program	 "boxshade"
Program	 "mrtrans"
Program	 "tcoffee"
Program	 "primer3"
Program	 "osp"
Program	 "ospX"
Program	 "MWCalculator"
Program	 "xylem_identify"
Program	 "entrez"
Program	 "nclever"
Program	 "fetch"
Program	 "ssearch"
Program	 "fastx"
Program	 "fasty"
Program	 "features"
Program	 "splitdb"
Program	 "getloc"
Program	 "shuffle"
Program	 "randseq"
Program	 "dbstat"
Program	 "gp"
Program	 "xland"
Program	 "consensus"
Program	 "wconsensus"
Program	 "patser"
Program	 "gmat-inf-gc"
Program	 "treetool"
Program	 "phylo_win"
Program	 "protpars"
Program	 "dnapars"
Program	 "dnamove"
Program	 "dnapenny"
Program	 "dnacomp"
Program	 "dnainvar"
Program	 "dnaml"
Program	 "fastDNAml"
Program	 "dnamlk"
Program	 "dnadist"
Program	 "protdist"
Program	 "seqboot"
Program	 "fitch"
Program	 "kitsch"
Program	 "neighbor"
Program	 "contml"
Program	 "contrast"
Program	 "gendist"
Program	 "restml"
Program	 "restdist"
Program	 "mix"
Program	 "move"
Program	 "penny"
Program	 "dollop"
Program	 "dolmove"
Program	 "dolpenny"
Program	 "clique"
Program	 "factor"
Program	 "drawgram"
Program	 "drawtree"
Program	 "consense"
Program	 "blastcl3"
Program	 "Mapmaker"
Program	 "MapmakerQTL"
Program	 "artemis"
Program	 "xace"
Program	 "tace"
Program	 "pars"
Program	 "treedist"
Program	 "acedemo"



 // End of this dump file