Text : "Object-oriented biological database engine"
Text : "DNA sequence annotation"
Text : "Multiple sequence alignment"
Text : "Create consensus patterns from unaligned sequences"
Text : "Gel image analysis and annotation"
Text : "Sequence chromatogram viewer"
Text : "Pairwise and global similarity searches"
Text : "Maximum likelihood sequence phylogeny"
Text : "Programs and API for phylogeny"
Text : "Sequence analysis tools"
Text : "Codon usage analysis"
Text : "Genetic Data Environment"
Text : "Parse a DNA sequence into introns and exons"
Text : "Multiple alignment display"
Text : "Find subcloning strategies"
Text : "Mapping with molecular and phenotypic markers"
Text : "Multiple alignment viewer"
Text : "Oligonucleotide Molecular Weight Calculator"
Text : "Database tools - Natl. Ctr. for Biotech. Information"
Text : "Sequence retrieval"
Text : "Oligonucleotide design"
Text : "Package for Inferring Phylogenies"
Text : "Phylogenetic analysis"
Text : "Sequence format translator"
Text : "Restriction digest analysis"
Text : "Phylogenetic tree editor"
Text : "Find motifs in a group of sequences"
Text : "Create and manipulate database subsets"
Text : "Main Phylip documentation file"
Text : "Continuous character programs"
Text : "Discrete (0,1) character programs"
Text : "Distance matrix programs"
Text : "Tree drawing programs"
Text : "Sequence phylogeny programs"
Text : "Data Preparation Guide"
Text : "User's Guide"
Text : "Documentation"
Text : "Manual"
Text : "REBASE TypeII restriction enzymes"
Text : "Tutorial"
Text : "Tutorial commands for mouse data"
Text : "Initilization file for mouse data"
Text : "Mouse F2 - 308 markers, 46 progeny"
Text : "Tutorial commands from sample data"
Text : "Sample F2 data"
Text : "Parse features from GenBank flatfiles"
Text : "Keyword search on local flatfile database"
Text : "Translate nucleic acid to protein"
Text : "Reverse translate protein to degenerate DNA"
Text : "Translate multiply aligned sequences in clustal format to Intelligenetics format"
Text : "print a multiple alignment using plain text"
Text : "used by FINDKEY to extract LOCUS names from database hits"
Text : "retrieve entries from local flatfile database by name or accession number"
Text : "extract features from GenBank flatfile entries"
Text : "split a GenBank flatfile into a database containing annotation, sequence and index"
Text : "retrieve entries from a local flatfile database"
Text : "randomize sequences using a sliding window"
Text : "Calculates amino acid frequencies for one or more proteins"
Text : "Sequence dislpay and manipulation"
Text : "Restriction site search"
Text : "Reformats a free-format or FASTA-format file to a fixed line-length, preserving comments that begin with a semicolon (\;)"
Text : "Calculates restriction sites, fragments and fragment ends for multiple enzyme digests, complete or partial"
Text : "Given migration distances for standards of know size, calculate sizes of unknown fragments"
Text : "Dot-matrix protein similarity, k=1"
Text : "Dot-matrix protein similarity, k=2"
Text : "Dot-matrix DNA similarity, k=3"
Text : "Dot-matrix DNA similarity, k=4"
Text : "Find protein coding regions using method of Fickett"
Text : "Annotate and submit sequences to GenBank"
Text : "Protein 3D structure viewer"
Text : "Find and Retrieve Data from NCBI"
Text : "run BLAST remotely at NCBI"
Text : "Statistical significance of pairwise similarities"
Text : "Calculate molecular weights for oligonucleotides"
Text : "Protein parsimony"
Text : "DNA parsimony"
Text : "DNA parsimony with interactive tree rearrangement"
Text : "DNA parsimony using branch and bound method"
Text : "DNA phylogeny using compatability method"
Text : "DNA sequence phylogeny invariants"
Text : "DNA phylogeny using Maximum Likelihood"
Text : "DNA phylogeny using Maximum Likelihood (with evolutionary clock)"
Text : "Construct distance matrix for DNA sequences"
Text : "Construct distance matrix for protein sequences"
Text : "Create resampled datasets"
Text : "Distance trees - Fitch\/ Margoliash"
Text : "Distance trees - Fitch\/ Margoliash (molecular clock)"
Text : "Distance trees - Neighbor-Joining\/UPGMA"
Text : "Discrete data parsimony method of DOLLO"
Text : "Draw cladograms"
Text : "Draw radial trees"
Text : "Consensus trees"
Text : "Discrete character parsimony"
Text : "Calculate distance between trees"
Text : "Draw and edit phylogenetic trees"
Text : "Create genetic maps using marker and phenotype data"
Text : "Create maps for QTL data"
Text : "DNA sequence annotation tool"
Text : "Graphic interface to ACeDB"
Text : "text interface to ACeDB"
Text : "Demonstration laboratory database"
Table : "Packages"
Table : "Categories"
Table : "Programs"
Package : "ACeDB"
Package : "ARTEMIS"
Package : "CLUSTAL"
Package : "CONSENSUS"
Package : "DNA-GUI"
Package : "EBI"
Package : "FASTA"
Package : "FASTDNAML"
Package : "forester"
Package : "FSAP"
Package : "GCUA"
Package : "GDE"
Package : "GENEPARSER"
Package : "ISREC"
Package : "LINDENBAUM"
Package : "Mapmaker"
Package : "MCLAMP"
Package : "MWC"
Package : "NCBI"
Package : "OGMP"
Package : "OSP"
Package : "PHYLIP"
Package : "PHYLO_WIN"
Package : "PRIMER3"
Package : "READSEQ"
Package : "TACG"
Package : "TCOFFEE"
Package : "TREETOOL"
Package : "XLANDSCAPE"
Package : "XYLEM"
Category : "Database"
Category : "Sequence - Multiple Alignment"
Category : "Sequence - Pattern Discovery and Matching"
Category : "Phylogeny"
Category : "Sequence - Phylogeny"
Category : "Sequence"
Category : "Sequence - Annotation and Gene Discovery"
Category : "Genetics"
Category : "Molecular Markers"
Category : "Sequence - Oligonucleotides"
Category : "Sequence - Protein"
Category : "Sequence - Protein Structure"
Category : "Sequence - Pairwise Similarity"
Category : "Sequence - DNA Sequencing"
Category : "Sequence - File Formatting"
Category : "Sequence - Restriction Analysis"
Category : "Gel Electrophoresis"
File : "$doc\/acedb\/acedb-man-0.pdf"
File : "$doc\/forester\/NHX.pdf"
File : "$doc\/mapmaker\/DataPreparationGuide.txt"
File : "$doc\/Phylip\/main.html"
File : "$doc\/Phylip\/contchar.html"
File : "$doc\/Phylip\/discrete.html"
File : "$doc\/Phylip\/distance.html"
File : "$doc\/Phylip\/draw.html"
File : "$doc\/Phylip\/sequence.html"
File : "$doc\/fsap\/numseq.asc"
File : "$doc\/GDE\/GDE2.2_manual.ps"
File : "$doc\/entrez\/sequin.htm"
File : "$doc\/EBI\/trace_viewer_paper.html"
File : "$doc\/GDE\/CAP2.help"
File : "$doc\/fsap\/numseq.txt"
File : "$doc\/xylem\/ribosome.txt"
File : "$doc\/xylem\/prot2nuc.txt"
File : "$doc\/readseq\/readseq.asc"
File : "$doc\/readseq\/readseq-help.html"
File : "$doc\/readseq\/Readseq2-help.html"
File : "$doc\/fasta\/format.asc"
File : "$doc\/fsap\/funnel.as"
File : "$doc\/clustalw\/clu2ig.txt"
File : "$doc\/fsap\/rest.txt"
File : "$doc\/fsap\/digest.txt"
File : "$doc\/fsap\/gel.txt"
File : "$doc\/tacg\/tacg.main.html"
File : "$doc\/cloneit.html"
File : "$doc\/DNA-GUI\/dnagui_ug.html"
File : "$doc\/DNA-GUI\/guide.ps"
File : "$doc\/fsap\/prostat.txt"
File : "$doc\/fasta\/fasta.asc"
File : "$doc\/fasta\/fasta.as"
File : "http:\/\/www.ncbi.nlm.nih.gov\/Structure\/CN3D\/cn3d.shtml"
File : "$doc\/fsap\/hom.txt"
File : "$doc\/fasta\/fasta20.asc"
File : "$doc\/gcua\/codon.hlp"
File : "$doc\/fsap\/testcode.txt"
File : "$doc\/clustalw\/clustalw.asc"
File : "$doc\/clustalx\/clustalx.htm"
File : "$doc\/xylem\/reform.txt"
File : "$doc\/jalview\/help.html"
File : "$doc\/boxshade.asc"
File : "$doc\/fasta\/mrtrans.txt"
File : "$doc\/tcoffee\/t_coffee_doc.html"
File : "$doc\/tcoffee\/t_coffee_doc.pdf"
File : "$doc\/primer\/primer3.html"
File : "$doc\/primer\/primer3.ps"
File : "$doc\/primer\/example"
File : "$doc\/osp\/INSTR.asc"
File : "http:\/\/www-classes.cs.uchicago.edu\/~gluc\/MWC\/MWC.html"
File : "$doc\/xylem\/findkey.txt"
File : "$doc\/xylem\/identify.txt"
File : "$doc\/entrez\/entrzdoc.txt"
File : "$doc\/nclever\/nclever_manual.txt"
File : "$doc\/xylem\/fetch.txt"
File : "$doc\/xylem\/features.txt"
File : "$doc\/xylem\/splitdb.txt"
File : "$doc\/xylem\/getloc.txt"
File : "$doc\/xylem\/getob.txt"
File : "$doc\/xylem\/shuffle.txt"
File : "$doc\/xylem\/dbstat.txt"
File : "$doc\/geneparser\/GeneParser.asc"
File : "$doc\/XLandscape\/readme.txt"
File : "$doc\/Consensus\/consensus.asc"
File : "$doc\/Consensus\/wconsensus.asc"
File : "$doc\/Consensus\/patser.asc"
File : "$doc\/Consensus\/gmat-inf-gc.asc"
File : "$doc\/treetool.txt"
File : "$doc\/Phylip\/fastDNAml\/fastDNAml_doc.txt"
File : "http:\/\/pbil.univ-lyon1.fr\/software\/phylowin.html"
File : "http:\/\/www-igbmc.u-strasbg.fr\/BioInfo\/ClustalW\/"
File : "$doc\/fasta\/fasta3x.asc"
File : "http:\/\/www.people.virginia.edu\/~wrp\/"
File : "http:\/\/evolution.genetics.washington.edu\/phylip.html"
File : "$doc\/Phylip\/drawgram.html"
File : "$dat\/REBASE\/type2.lst"
File : "$doc\/fsap\/funnel.txt"
File : "$doc\/NCBI\/netblast\/netblast.txt"
File : "$doc\/Phylip\/clique.html"
File : "$doc\/Phylip\/consense.html"
File : "$doc\/Phylip\/contml.html"
File : "$doc\/Phylip\/contrast.html"
File : "$doc\/Phylip\/dnacomp.html"
File : "$doc\/Phylip\/dnadist.html"
File : "$doc\/Phylip\/dnainvar.html"
File : "$doc\/Phylip\/dnaml.html"
File : "$doc\/Phylip\/dnamlk.html"
File : "$doc\/Phylip\/dnamove.html"
File : "$doc\/Phylip\/dnapars.html"
File : "$doc\/Phylip\/dnapenny.html"
File : "$doc\/Phylip\/dolboot.html"
File : "$doc\/Phylip\/dollop.html"
File : "$doc\/Phylip\/dolmove.html"
File : "$doc\/Phylip\/dolpenny.html"
File : "$doc\/Phylip\/drawtree.html"
File : "$doc\/Phylip\/factor.html"
File : "$doc\/Phylip\/fitch.html"
File : "$doc\/Phylip\/gendist.html"
File : "$doc\/Phylip\/kitsch.html"
File : "$doc\/Phylip\/mix.html"
File : "$doc\/Phylip\/move.html"
File : "$doc\/Phylip\/neighbor.html"
File : "$doc\/Phylip\/penny.html"
File : "$doc\/Phylip\/protdist.html"
File : "$doc\/Phylip\/protpars.html"
File : "$doc\/Phylip\/restdist.html"
File : "$doc\/Phylip\/restml.html"
File : "$doc\/Phylip\/seqboot.html"
File : "$doc\/forester\/atv_documentation.pdf"
File : "$doc\/mapmaker\/mapmaker.refguide.pdf"
File : "$doc\/mapmaker\/mapmaker.tutorial.pdf"
File : "$doc\/mapmaker\/mapmakerQTL.tutorial.pdf"
File : "$doc\/mapmaker\/mapmakerqtl.refguide.pdf"
File : "$doc\/mapmaker\/mapmaker.refguide.ps"
File : "$doc\/mapmaker\/mapmaker.tutorial.ps"
File : "$doc\/mapmaker\/mapmakerQTL.tutorial.ps"
File : "$doc\/mapmaker\/mapmakerqtl.refguide.ps"
File : "$dat\/mapmaker\/mouse.in"
File : "$dat\/mapmaker\/mouse.prep"
File : "$dat\/mapmaker\/mouse.raw"
File : "$dat\/mapmaker\/sample.in"
File : "$dat\/mapmaker\/sample.inp"
File : "$dat\/mapmaker\/sample.inq"
File : "$dat\/mapmaker\/sample.raw"
File : "$tutorials\/GDE\/sequence\/sequence.html"
File : "$tutorials\/GDE\/dotmatrix\/dotmatrix.html"
File : "$doc\/artemis\/manual\/index.shtml"
File : "$tutorials\/GDE\/keywords\/keywords.html"
File : "$tutorials\/GDE\/dataset\/dataset.html"
File : "$tutorials\/GDE\/database.sim\/database.sim.html"
File : "$tutorials\/GDE\/discrete\/discrete.html"
File : "$tutorials\/GDE\/multalign\/multalign.html"
File : "$tutorials\/GDE\/pairwise.sim\/pairwise.sim.html"
File : "$doc\/Phylip\/retree.html"
File : "$doc\/Phylip\/treedist.html"
File : "$doc\/Phylip\/pars.html"
File : "$doc\/fasta\/prss.txt"
File : "$doc\/fasta\/prdf.txt"
Program : "xace"
Program : "tace"
Program : "acedemo"
Program : "artemis"
Program : "clustalw"
Program : "clustalx"
Program : "consensus"
Program : "wconsensus"
Program : "patser"
Program : "gmat-inf-gc"
Program : "dui"
Program : "TraceView"
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"
Program : "fastDNAml"
Program : "atv"
Program : "numseq"
Program : "intrest"
Program : "bachrest"
Program : "funnel"
Program : "digest"
Program : "gel"
Program : "prostat"
Program : "p1hom"
Program : "p2hom"
Program : "d3hom"
Program : "d4hom"
Program : "testcode"
Program : "gcua"
Program : "gde"
Program : "CAP2"
Program : "gp"
Program : "boxshade"
Program : "CloneIt"
Program : "Mapmaker"
Program : "MapmakerQTL"
Program : "Jalview"
Program : "MWCalculator"
Program : "sequin"
Program : "Cn3D"
Program : "entrez"
Program : "blastcl3"
Program : "nclever"
Program : "osp"
Program : "ospX"
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"
Program : "phylo_win"
Program : "primer3"
Program : "readseq"
Program : "tacg"
Program : "tcoffee"
Program : "treetool"
Program : "xland"
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 : "solaris-sparc"
Platform : "linux-intel"
