Program Index

• acedemo - Demonstration laboratory database
• align - Pairwise global sequence alignment
• ArrayNorm - Normalize gene array data
• artemis - DNA sequence annotation tool
• atv - Draw and edit phylogenetic trees
• bachrest - Restriction site search (batch)
• bestscor - Calculate the score of a 100% identical match
• biolegato - Programmable graphic interface
• birchconfig - BIRCH install wizard
• birchdb - BIRCH documentation database
• birchhome.sh - modify paths in BIRCH parameter files for local BIRCH system
• birchstats - Report statistics on BIRCH usage
• blastcl3 - run BLAST remotely at NCBI
• BLExtractSubset.py - Extract a subset of sequences from a GDE flatfile
• blrevcomp - reverse-complement, reverse or complement a DNA or RNA strand
• bluejay - Genome visualization and annotation
• boxshade - Multiple alignment display
• browser.csh - Launch a default browser from another application
• btail.csh - Print the contents of a file beginning at line x
• CAP2 - Contig assembly program
• clique - Compatability method for two-state characters
• CloneIt - Find subcloning strategies
• clu2ig - Translate multiply aligned sequences in clustal format to Intelligenetics format
• clustalw - Multiple sequence alignment
• clustalx - Multiple sequence alignment and editing
• Cn3D - Protein 3D structure viewer
• consense - Consensus trees
• consensus - Consensus patterns in unaligned sequences (user-defined pattern width)
• contml - Gene Frequencies and Continuous Characters Maximum Likelihood
• contrast - compute contrasts for comparative method
• csv2phyl.sh - Convert molecular marker data from csv format to Phylip format
• customdoc.py - String substitution for HTML files
• d3hom - Dot-matrix DNA similarity, k=3
• d4hom - Dot-matrix DNA similarity, k=4
• dat2ace.sh - Create ACeDB file objects for all data files in a directory
• dbstat - Calculates amino acid frequencies for one or more proteins
• dGDE - GDE interface for leash
• dialign-tx - segment-based multiple alignment
• dnacomp - DNA phylogeny using compatability method
• dnadist - Construct distance matrix for DNA sequences
• dnainvar - DNA sequence phylogeny invariants
• dnaml - DNA phylogeny using Maximum Likelihood
• dnamlk - DNA phylogeny using Maximum Likelihood (with evolutionary clock)
• dnamove - DNA parsimony with interactive tree rearrangement
• dnapars - DNA parsimony
• dnapenny - DNA parsimony using branch and bound method
• doc2ace.sh - Create ACeDB file objects for all documenataion files in a directory
• dollop - Discrete data parsimony method of DOLLO
• dolmove - Interactive Dollo and Polymorphism Parsimony
• dolpenny - Branch and bound parsimony using Dollo and polymorphism methods
• drawgram - Draw cladograms
• drawtree - Draw radial trees
• ExpressConverter - Convert microarray files to TIGR file formats
• factor - Generate discrete (0,1) characters from multistate characters
• fasta - Sequence database similarity
• fastDNAml - DNA maximum likelihood
• fastf - compare mixed peptides to a protein database
• fastm - compare ordered peptides (or short DNA sequences) to a protein or DNA database
• fasts - compare unordered peptides to a protein database
• fastx - Database similarity - allow frameshifts between codons
• fasty - Database similarity - Allow frameshifts within codons
• features - extract features from GenBank flatfile entries
• fetch - retrieve entries from local flatfile database by name or accession number
• fil.py - create .fil files for use by FASTA
• findkey - Keyword search on local flatfile database
• fitch - Distance trees - Fitch/ Margoliash
• flat2phyl - Convert a GDE flatfile into a Phylip discrete character file
• fromgb -
• funnel - Reformats a free-format or FASTA-format file to a fixed line-length, preserving comments that begin with a semicolon (;)
• garnier - Protein secondary structure
• gbupdate - download and update GenBank flatfile database
• gcua - General codon and amino acid usage analysis
• gde - Genetic Data Environment
• gel - Given migration distances for standards of know size, calculate sizes of unknown fragments
• gendist - Compute genetic distances from gene frequencies
• genographer - Score markers from gel images
• getloc - retrieve entries from a local flatfile database
• getob - Parse features from GenBank flatfiles
• ggsearch - global alignment of two DNA or protein sequences
• glsearch - global alignment of DNA or protein query sequence with local alignments of database sequences
• gmat-inf-gc - Information content of an alignment matrix
• gp - Parse a DNA sequence into introns and exons
• grease - Protein hydrophobicity
• htmldoc.py - Create BIRCH HTML documentation from BIRCH and local databases
• intrest - Restriction site search
• Jalview - Multiple alignment viewer
• kitsch - Distance trees - Fitch/ Margoliash (molecular clock)
• lalign - Rigorous local pairwise alignment
• lbirchdb - Database for local documentation
• leash - command line interface for SeqHound API
• lgbirchdb - Empty database to be used for local-installed documentation
• MakeCons - Create a consensus sequence from a multiple alignment
• makemenus.py - Create .GDEmenus files for all platforms
• Mapmaker - Create genetic maps using marker and phenotype data
• MapmakerQTL - Create maps for QTL data
• mbiolegato - bioLegato interface for discrete state data (eg. molecular markers)
• mesquite - A modular system for evolutionary analysis
• mGDE - GDE interface for discrete state data (eg. molecular markers)
• midas - Microarray Data Analysis System
• mix - Mixed method discrete character parsimony
• move - Interactive mixed-method parsimony
• mrbayes - Bayesian inference of phylogeny
• mrtrans - Align DNA sequences to a protein multiple alignment
• multidigest - Calculates restriction sites, fragments and fragment ends for multiple enzyme digests, complete or partial
• MWCalculator - Calculate molecular weights for oligonucleotides
• nclever - Network command-line Entrez
• neighbor - Distance trees - Neighbor-Joining/UPGMA
• numseq - Sequence dislpay and manipulation
• osp - Oligonucleotide Search Program
• ospX - Oligonucleotide search program
• p1hom - Dot-matrix protein similarity, k=1
• p2hom - Dot-matrix protein similarity, k=2
• pars - Discrete character parsimony
• patser - Score the match of a sequence with an alignment matrix
• penny - Branch and bound parsimony for discrete data
• phyl2flat - Convert a Phylip discrete character file into a GDE flatfile
• pirupdate - download and update PIR flatfile database
• primer3 - Primer design and evaluation
• prostat - Calculates amino acid frequencies for one or more proteins
• prot2nuc - Reverse translate protein to degenerate DNA
• protdist - Construct distance matrix for protein sequences
• protpars - Protein parsimony
• randseq - Randomize a set of sequences
• readseq - Convert sequence files to other formats
• reform - print a multiple alignment using plain text
• relate - Statistical significance of database similarity
• restdist - Compute distance matrices for discrete data
• restml - Maximum likelihood phylogeny for discrete data
• reticulate - Detect reticulate evolution by DNA compatability
• ribosome - Translate nucleic acid to protein
• ruler - Print a text ruler for use in numbering columns
• seqboot - Create resampled datasets
• sequin - Annotate and submit sequences to GenBank
• shuffle - randomize sequences using a sliding window
• splitdb - split a GenBank flatfile into a database containing annotation, sequence and index
• ssearch - Rigorous Smith-Waterman database similarity search
• tace - text interface to ACeDB
• tacg - Restriction and pattern mapping
• taverna - Graphic workflow designer
• tbiolegato - bioLegato interface for phylogenetic trees
• tcoffee - Multiple sequence alignment
• testcode - Find protein coding regions using method of Fickett
• tfasta - Database similarity with translated DNA database
• tfastf - compare mixed peptides to a translated DNA database
• tfasts - compare unordered peptides to a translated DNA database
• tfastx - compare a protein to a DNA database, calculating similarities with frameshifts
• tfasty - compare a protein to a DNA database, calculating similarities with frameshifts
• tGDE - GDE interface for phylogenetic trees
• tmev - TIGR Multi-Experiment Viewer
• TraceView - Sequence chromatogram viewer
• treedist - Calculate distance between trees
• treetool - Phylogenetic tree editor
• UNINSTALL-birch.sh - Uninstall a BIRCH system
• wconsensus - Consensus pattern in unaligned sequences (automatic pattern width)
• weighbor - weighted neighbor joining
• xace - Graphic interface to ACeDB
• xylem_identify - used by FINDKEY to extract LOCUS names from database hits