ALPHABETIC LIST OF PROGRAMS

Program name Description
aaindexextract Extract amino acid property data from AAINDEX
abiview Display the trace in an ABI sequencer file
acdc Test an application ACD file
acdpretty Correctly reformat an application ACD file
acdtable Generate an HTML table of parameters from an application ACD file
acdtrace Trace processing of an application ACD file (for testing)
acdvalid Validate an application ACD file
aligncopy Reads and writes alignments
aligncopypair Reads and writes pairs from alignments
antigenic Finds antigenic sites in proteins
backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq Back-translate a protein sequence to a nucleotide sequence
banana Plot bending and curvature data for B-DNA
biosed Replace or delete sequence sections
btwisted Calculate the twisting in a B-DNA sequence
cai Calculate codon adaptation index
chaos Draw a chaos game representation plot for a nucleotide sequence
charge Draw a protein charge plot
checktrans Reports STOP codons and ORF statistics of a protein
chips Calculates Nc codon usage statistic
cirdna Draws circular maps of DNA constructs
codcmp Codon usage table comparison
codcopy Copy and reformat a codon usage table
coderet Extract CDS, mRNA and translations from feature tables
compseq Calculate the composition of unique words in sequences
cons Create a consensus sequence from a multiple alignment
consambig Create an ambiguous consensus sequence from a multiple alignment
cpgplot Identify and plot CpG islands in nucleotide sequence(s)
cpgreport Identify and report CpG-rich regions in nucleotide sequence(s)
cusp Create a codon usage table from nucleotide sequence(s)
cutgextract Extract codon usage tables from from CUTG database
cutseq Removes a section from a sequence
dan Calculates nucleic acid melting temperature
dbiblast Index a BLAST database
dbifasta Index a fasta file database
dbiflat Index a flat file database
dbigcg Index a GCG formatted database
dbxfasta Index a fasta file database using b+tree indices
dbxflat Index a flat file database using b+tree indices
dbxgcg Index a GCG formatted database using b+tree indices
degapseq Removes non-alphabetic (e.g. gap) characters from sequences
density Draw a nucleic acid density plot
descseq Alter the name or description of a sequence
diffseq Compare and report features of two similar sequences
digest Reports on protein proteolytic enzyme or reagent cleavage sites
distmat Create a distance matrix from a multiple sequence alignment
dotmatcher Draw a threshold dotplot of two sequences
dotpath Draw a non-overlapping wordmatch dotplot of two sequences
dottup Displays a wordmatch dotplot of two sequences
dreg Regular expression search of nucleotide sequence(s)
edialign Local multiple alignment of sequences
ehmmalign Align sequences to an HMM profile
ehmmbuild Build a profile HMM from an alignment
ehmmcalibrate Calibrate HMM search statistics
ehmmconvert Convert between profile HMM file formats
ehmmemit Generate sequences from a profile HMM
ehmmfetch Retrieve an HMM from an HMM database
ehmmindex Create a binary SSI index for an HMM database
ehmmpfam Search one or more sequences against an HMM database
ehmmsearch Search a sequence database with a profile HMM
einverted Finds inverted repeats in nucleotide sequences
emast Motif detection
embossdata Find and retrieve EMBOSS data files
embossversion Writes the current EMBOSS version number to a file
ememe Motif detection
emma Multiple sequence alignment (ClustalW wrapper)
emowse Search protein sequences by digest fragment molecular weight
entret Retrieves sequence entries from flatfile databases and files
epestfind Finds PEST motifs as potential proteolytic cleavage sites
eprimer3 Picks PCR primers and hybridization oligos
equicktandem Finds tandem repeats in nucleotide sequences
esim4 Align an mRNA to a genomic DNA sequence
est2genome Align EST sequences to genomic DNA sequence
etandem Finds tandem repeats in a nucleotide sequence
extractalign Extract regions from a sequence alignment
extractfeat Extract features from sequence(s)
extractseq Extract regions from a sequence
fclique Largest clique program
fconsense Majority-rule and strict consensus tree
fcontml Gene frequency and continuous character Maximum Likelihood
fcontrast Continuous character Contrasts
fdiscboot Bootstrapped discrete sites algorithm
fdnacomp DNA compatibility algorithm
fdnadist Nucleic acid sequence Distance Matrix program
fdnainvar Nucleic acid sequence Invariants method
fdnaml Estimates nucleotide phylogeny by maximum likelihood
fdnamlk Estimates nucleotide phylogeny by maximum likelihood
fdnamove Interactive DNA parsimony
fdnapars DNA parsimony algorithm
fdnapenny Penny algorithm for DNA
fdollop Dollo and polymorphism parsimony algorithm
fdolmove Interactive Dollo or Polymorphism Parsimony
fdolpenny Penny algorithm Dollo or polymorphism
fdrawgram Plots a cladogram- or phenogram-like rooted tree diagram
fdrawtree Plots an unrooted tree diagram
featcopy Reads and writes a feature table
featreport Reads and writes a feature table
ffactor Multistate to binary recoding program
ffitch Fitch-Margoliash and Least-Squares Distance Methods
ffreqboot Bootstrapped genetic frequencies algorithm
fgendist Compute genetic distances from gene frequencies
findkm Calculate and plot enzyme reaction data
fkitsch Fitch-Margoliash method with contemporary tips
fmix Mixed parsimony algorithm
fmove Interactive mixed method parsimony
fneighbor Phylogenies from distance matrix by N-J or UPGMA method
fpars Discrete character parsimony
fpenny Penny algorithm, branch-and-bound
fproml Protein phylogeny by maximum likelihood
fpromlk Protein phylogeny by maximum likelihood
fprotdist Protein distance algorithm
fprotpars Protein parsimony algorithm
freak Generate residue/base frequency table or plot
frestboot Bootstrapped restriction sites algorithm
frestdist Distance matrix from restriction sites or fragments
frestml Restriction site maximum Likelihood method
fretree Interactive tree rearrangement
fseqboot Bootstrapped sequences algorithm
fseqbootall Bootstrapped sequences algorithm
ftreedist Distances between trees
ftreedistpair Distances between two sets of trees
fuzznuc Search for patterns in nucleotide sequences
fuzzpro Search for patterns in protein sequences
fuzztran Search for patterns in protein sequences (translated)
garnier Predicts protein secondary structure using GOR method
geecee Calculate fractional GC content of nucleic acid sequences
getorf Finds and extracts open reading frames (ORFs)
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
hmoment Calculate and plot hydrophobic moment for protein sequence(s)
iep Calculate the isoelectric point of proteins
infoalign Display basic information about a multiple sequence alignment
infoseq Display basic information about sequences
isochore Plots isochores in DNA sequences
jaspextract Extract data from JASPAR
jaspscan Scans DNA sequences for transcription factors
lindna Draws linear maps of DNA constructs
listor Write a list file of the logical OR of two sets of sequences
makenucseq Create random nucleotide sequences
makeprotseq Create random protein sequences
marscan Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
maskambignuc Masks all ambiguity characters in nucleotide sequences with N
maskambigprot Masks all ambiguity characters in protein sequences with X
maskfeat Write a sequence with masked features
maskseq Write a sequence with masked regions
matcher Waterman-Eggert local alignment of two sequences
megamerger Merge two large overlapping DNA sequences
merger Merge two overlapping sequences
msbar Mutate a sequence
mwcontam Find weights common to multiple molecular weights files
mwfilter Filter noisy data from molecular weights file
needle Needleman-Wunsch global alignment of two sequences
newcpgreport Identify CpG islands in nucleotide sequence(s)
newcpgseek Identify and report CpG-rich regions in nucleotide sequence(s)
newseq Create a sequence file from a typed-in sequence
nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file
noreturn Remove carriage return from ASCII files
nospace Remove all whitespace from an ASCII text file
notab Replace tabs with spaces in an ASCII text file
notseq Write to file a subset of an input stream of sequences
nthseq Write to file a single sequence from an input stream of sequences
octanol Draw a White-Wimley protein hydropathy plot
oddcomp Identify proteins with specified sequence word composition
palindrome Finds inverted repeats in nucleotide sequence(s)
pasteseq Insert one sequence into another
patmatdb Searches protein sequences with a sequence motif
patmatmotifs Scan a protein sequence with motifs from the PROSITE database
pepcoil Predicts coiled coil regions in protein sequences
pepinfo Plot amino acid properties of a protein sequence in parallel
pepnet Draw a helical net for a protein sequence
pepstats Calculates statistics of protein properties
pepwheel Draw a helical wheel diagram for a protein sequence
pepwindow Draw a Kyte-Doolittle hydropathy plot for a protein sequence
pepwindowall Draw Kyte-Doolittle hydropathy plot for a protein alignment
plotcon Plot conservation of a sequence alignment
plotorf Plot potential open reading frames in a nucleotide sequence
polydot Draw dotplots for all-against-all comparison of a sequence set
preg Regular expression search of protein sequence(s)
prettyplot Draw a sequence alignment with pretty formatting
prettyseq Write a nucleotide sequence and its translation to file
primersearch Search DNA sequences for matches with primer pairs
printsextract Extract data from PRINTS database for use by pscan
profit Scan one or more sequences with a simple frequency matrix
prophecy Create frequency matrix or profile from a multiple alignment
prophet Scan one or more sequences with a Gribskov or Henikoff profile
prosextract Processes the PROSITE motif database for use by patmatmotifs
pscan Scans protein sequence(s) with fingerprints from the PRINTS database
psiphi Calculates phi and psi torsion angles from protein coordinates
rebaseextract Process the REBASE database for use by restriction enzyme applications
recoder Find restriction sites to remove (mutate) with no translation change
redata Retrieve information from REBASE restriction enzyme database
remap Display restriction enzyme binding sites in a nucleotide sequence
restover Find restriction enzymes producing a specific overhang
restrict Report restriction enzyme cleavage sites in a nucleotide sequence
revseq Reverse and complement a nucleotide sequence
seealso Finds programs with similar function to a specified program
seqmatchall All-against-all word comparison of a sequence set
seqret Reads and writes (returns) sequences
seqretsplit Reads sequences and writes them to individual files
showalign Display a multiple sequence alignment in pretty format
showdb Displays information on configured databases
showfeat Display features of a sequence in pretty format
showorf Display a nucleotide sequence and translation in pretty format
showseq Displays sequences with features in pretty format
shuffleseq Shuffles a set of sequences maintaining composition
sigcleave Reports on signal cleavage sites in a protein sequence
silent Find restriction sites to insert (mutate) with no translation change
sirna Finds siRNA duplexes in mRNA
sixpack Display a DNA sequence with 6-frame translation and ORFs
sizeseq Sort sequences by size
skipredundant Remove redundant sequences from an input set
skipseq Reads and writes (returns) sequences, skipping first few
splitter Split sequence(s) into smaller sequences
stretcher Needleman-Wunsch rapid global alignment of two sequences
stssearch Search a DNA database for matches with a set of STS primers
supermatcher Calculate approximate local pair-wise alignments of larger sequences
syco Draw synonymous codon usage statictic plot for a nucleotide sequence
tcode Identify protein-coding regions using Fickett TESTCODE statistic
textsearch Search the textual description of sequence(s)
tfextract Process TRANSFAC transcription factor database for use by tfscan
tfm Displays full documentation for an application
tfscan Identify transcription factor binding sites in DNA sequences
tmap Predict and plot transmembrane segments in protein sequences
tranalign Generate an aligment of nucleic coding regions from aligned proteins
transeq Translate nucleic acid sequences
trimest Remove poly-A tails from nucleotide sequences
trimseq Remove unwanted characters from start and end of sequence(s)
twofeat Finds neighbouring pairs of features in sequence(s)
union Concatenate multiple sequences into a single sequence
vectorstrip Removes vectors from the ends of nucleotide sequence(s)
vrnaalifold RNA alignment folding
vrnaalifoldpf RNA alignment folding with partition
vrnacofold RNA cofolding
vrnacofoldconc RNA cofolding with concentrations
vrnacofoldpf RNA cofolding with partitioning
vrnadistance RNA distances
vrnaduplex RNA duplex calculation
vrnaeval RNA eval
vrnaevalpair RNA eval with cofold
vrnafold Calculate secondary structures of RNAs
vrnafoldpf Secondary structures of RNAs with partition
vrnaheat RNA melting
vrnainverse RNA sequences matching a structure
vrnalfold Calculate locally stable secondary structures of RNAs
vrnaplot Plot vrnafold output
vrnasubopt Calculate RNA suboptimals
water Smith-Waterman local alignment of sequences
whichdb Search all sequence databases for an entry and retrieve it
wobble Plot third base position variability in a nucleotide sequence
wordcount Count and extract unique words in DNA sequence(s)
wordfinder Match large sequences against one or more other sequences
wordmatch Finds regions of identity (exact matches) of two sequences
wossname Finds programs by keywords in their short description
yank Add a sequence reference (a full USA) to a list file