ACD

Program name Description
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

ALIGNMENT CONSENSUS

Program name Description
cons Create a consensus sequence from a multiple alignment
consambig Create an ambiguous consensus sequence from a multiple alignment
megamerger Merge two large overlapping DNA sequences
merger Merge two overlapping sequences

ALIGNMENT DIFFERENCES

Program name Description
diffseq Compare and report features of two similar sequences

ALIGNMENT DOT PLOTS

Program name Description
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
polydot Draw dotplots for all-against-all comparison of a sequence set

ALIGNMENT GLOBAL

Program name Description
esim4 Align an mRNA to a genomic DNA sequence
est2genome Align EST sequences to genomic DNA sequence
needle Needleman-Wunsch global alignment of two sequences
stretcher Needleman-Wunsch rapid global alignment of two sequences

ALIGNMENT LOCAL

Program name Description
matcher Waterman-Eggert local alignment of two sequences
seqmatchall All-against-all word comparison of a sequence set
supermatcher Calculate approximate local pair-wise alignments of larger sequences
water Smith-Waterman local alignment of sequences
wordfinder Match large sequences against one or more other sequences
wordmatch Finds regions of identity (exact matches) of two sequences

ALIGNMENT MULTIPLE

Program name Description
edialign Local multiple alignment of sequences
emma Multiple sequence alignment (ClustalW wrapper)
infoalign Display basic information about a multiple sequence alignment
plotcon Plot conservation of a sequence alignment
prettyplot Draw a sequence alignment with pretty formatting
showalign Display a multiple sequence alignment in pretty format
tranalign Generate an aligment of nucleic coding regions from aligned proteins

DISPLAY

Program name Description
abiview Display the trace in an ABI sequencer file
cirdna Draws circular maps of DNA constructs
lindna Draws linear maps of DNA constructs
pepnet Draw a helical net for a protein sequence
pepwheel Draw a helical wheel diagram for a protein sequence
prettyplot Draw a sequence alignment with pretty formatting
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
seealso Finds programs with similar function to a specified program
showalign Display a multiple sequence alignment in pretty format
showdb Displays information on configured databases
showfeat Display features of a sequence in pretty format
showseq Displays sequences with features in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
textsearch Search the textual description of sequence(s)

EDIT

Program name Description
aligncopy Reads and writes alignments
aligncopypair Reads and writes pairs from alignments
biosed Replace or delete sequence sections
codcopy Copy and reformat a codon usage table
cutseq Removes a section from a sequence
degapseq Removes non-alphabetic (e.g. gap) characters from sequences
descseq Alter the name or description of a sequence
entret Retrieves sequence entries from flatfile databases and files
extractalign Extract regions from a sequence alignment
extractfeat Extract features from sequence(s)
extractseq Extract regions from a sequence
featcopy Reads and writes a feature table
featreport Reads and writes a feature table
listor Write a list file of the logical OR of two sets of sequences
makenucseq Create random nucleotide sequences
makeprotseq Create random protein 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
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
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqret Reads and writes (returns) sequences
seqretsplit Reads sequences and writes them to individual files
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
trimest Remove poly-A tails from nucleotide sequences
trimseq Remove unwanted characters from start and end of sequence(s)
union Concatenate multiple sequences into a single sequence
vectorstrip Removes vectors from the ends of nucleotide sequence(s)
yank Add a sequence reference (a full USA) to a list file

ENZYME KINETICS

Program name Description
findkm Calculate and plot enzyme reaction data

FEATURE TABLES

Program name Description
coderet Extract CDS, mRNA and translations from feature tables
extractfeat Extract features from sequence(s)
maskfeat Write a sequence with masked features
showfeat Display features of a sequence in pretty format
twofeat Finds neighbouring pairs of features in sequence(s)

HMM

Program name Description
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

INFORMATION

Program name Description
infoalign Display basic information about a multiple sequence alignment
infoseq Display basic information about sequences
seealso Finds programs with similar function to a specified program
showdb Displays information on configured databases
textsearch Search the textual description of sequence(s)
tfm Displays full documentation for an application
whichdb Search all sequence databases for an entry and retrieve it
wossname Finds programs by keywords in their short description

NUCLEIC 2D STRUCTURE

Program name Description
einverted Finds inverted repeats in nucleotide sequences
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

NUCLEIC CODON USAGE

Program name Description
cai Calculate codon adaptation index
chips Calculates Nc codon usage statistic
codcmp Codon usage table comparison
cusp Create a codon usage table from nucleotide sequence(s)
syco Draw synonymous codon usage statictic plot for a nucleotide sequence

NUCLEIC COMPOSITION

Program name Description
banana Plot bending and curvature data for B-DNA
btwisted Calculate the twisting in a B-DNA sequence
chaos Draw a chaos game representation plot for a nucleotide sequence
compseq Calculate the composition of unique words in sequences
dan Calculates nucleic acid melting temperature
density Draw a nucleic acid density plot
freak Generate residue/base frequency table or plot
isochore Plots isochores in DNA sequences
sirna Finds siRNA duplexes in mRNA
wordcount Count and extract unique words in DNA sequence(s)

NUCLEIC CPG ISLANDS

Program name Description
cpgplot Identify and plot CpG islands in nucleotide sequence(s)
cpgreport Identify and report CpG-rich regions in nucleotide sequence(s)
geecee Calculate fractional GC content of nucleic acid sequences
newcpgreport Identify CpG islands in nucleotide sequence(s)
newcpgseek Identify and report CpG-rich regions in nucleotide sequence(s)

NUCLEIC GENE FINDING

Program name Description
getorf Finds and extracts open reading frames (ORFs)
marscan Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
plotorf Plot potential open reading frames in a nucleotide sequence
showorf Display a nucleotide sequence and translation in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
syco Draw synonymous codon usage statictic plot for a nucleotide sequence
tcode Identify protein-coding regions using Fickett TESTCODE statistic
wobble Plot third base position variability in a nucleotide sequence

NUCLEIC MOTIFS

Program name Description
dreg Regular expression search of nucleotide sequence(s)
fuzznuc Search for patterns in nucleotide sequences
fuzztran Search for patterns in protein sequences (translated)
marscan Finds matrix/scaffold recognition (MRS) signatures in DNA sequences

NUCLEIC MUTATION

Program name Description
msbar Mutate a sequence
shuffleseq Shuffles a set of sequences maintaining composition

NUCLEIC PRIMERS

Program name Description
eprimer3 Picks PCR primers and hybridization oligos
primersearch Search DNA sequences for matches with primer pairs
stssearch Search a DNA database for matches with a set of STS primers

NUCLEIC PROFILES

Program name Description
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

NUCLEIC REPEATS

Program name Description
einverted Finds inverted repeats in nucleotide sequences
equicktandem Finds tandem repeats in nucleotide sequences
etandem Finds tandem repeats in a nucleotide sequence
palindrome Finds inverted repeats in nucleotide sequence(s)

NUCLEIC RESTRICTION

Program name Description
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
showseq Displays sequences with features in pretty format
silent Find restriction sites to insert (mutate) with no translation change

NUCLEIC RNA FOLDING

Program name Description
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

NUCLEIC TRANSCRIPTION

Program name Description
jaspscan Scans DNA sequences for transcription factors
tfscan Identify transcription factor binding sites in DNA sequences

NUCLEIC TRANSLATION

Program name Description
backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq Back-translate a protein sequence to a nucleotide sequence
coderet Extract CDS, mRNA and translations from feature tables
plotorf Plot potential open reading frames in a nucleotide sequence
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
showorf Display a nucleotide sequence and translation in pretty format
showseq Displays sequences with features in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
transeq Translate nucleic acid sequences

PHYLOGENY CONSENSUS

Program name Description
fconsense Majority-rule and strict consensus tree
ftreedist Distances between trees
ftreedistpair Distances between two sets of trees

PHYLOGENY CONTINUOUS CHARACTERS

Program name Description
fcontrast Continuous character Contrasts

PHYLOGENY DISCRETE CHARACTERS

Program name Description
fclique Largest clique program
fdollop Dollo and polymorphism parsimony algorithm
fdolpenny Penny algorithm Dollo or polymorphism
ffactor Multistate to binary recoding program
fmix Mixed parsimony algorithm
fmove Interactive mixed method parsimony
fpars Discrete character parsimony
fpenny Penny algorithm, branch-and-bound

PHYLOGENY DISTANCE MATRIX

Program name Description
ffitch Fitch-Margoliash and Least-Squares Distance Methods
fkitsch Fitch-Margoliash method with contemporary tips
fneighbor Phylogenies from distance matrix by N-J or UPGMA method

PHYLOGENY GENE FREQUENCIES

Program name Description
fcontml Gene frequency and continuous character Maximum Likelihood
fgendist Compute genetic distances from gene frequencies

PHYLOGENY MOLECULAR SEQUENCE

Program name Description
distmat Create a distance matrix from a multiple sequence alignment
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
fdolmove Interactive Dollo or Polymorphism Parsimony
ffreqboot Bootstrapped genetic frequencies algorithm
fproml Protein phylogeny by maximum likelihood
fpromlk Protein phylogeny by maximum likelihood
fprotdist Protein distance algorithm
fprotpars Protein parsimony algorithm
frestboot Bootstrapped restriction sites algorithm
frestdist Distance matrix from restriction sites or fragments
frestml Restriction site maximum Likelihood method
fseqboot Bootstrapped sequences algorithm
fseqbootall Bootstrapped sequences algorithm

PHYLOGENY TREE DRAWING

Program name Description
fdrawgram Plots a cladogram- or phenogram-like rooted tree diagram
fdrawtree Plots an unrooted tree diagram
fretree Interactive tree rearrangement

PROTEIN 2D STRUCTURE

Program name Description
garnier Predicts protein secondary structure using GOR method
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
hmoment Calculate and plot hydrophobic moment for protein sequence(s)
pepcoil Predicts coiled coil regions in protein sequences
pepnet Draw a helical net for a protein sequence
pepwheel Draw a helical wheel diagram for a protein sequence
tmap Predict and plot transmembrane segments in protein sequences

PROTEIN 3D STRUCTURE

Program name Description
psiphi Calculates phi and psi torsion angles from protein coordinates

PROTEIN COMPOSITION

Program name Description
backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq Back-translate a protein sequence to a nucleotide sequence
charge Draw a protein charge plot
checktrans Reports STOP codons and ORF statistics of a protein
compseq Calculate the composition of unique words in sequences
emowse Search protein sequences by digest fragment molecular weight
freak Generate residue/base frequency table or plot
iep Calculate the isoelectric point of proteins
mwcontam Find weights common to multiple molecular weights files
mwfilter Filter noisy data from molecular weights file
octanol Draw a White-Wimley protein hydropathy plot
pepinfo Plot amino acid properties of a protein sequence in parallel
pepstats Calculates statistics of protein properties
pepwindow Draw a Kyte-Doolittle hydropathy plot for a protein sequence
pepwindowall Draw Kyte-Doolittle hydropathy plot for a protein alignment
wordcount Count and extract unique words in DNA sequence(s)

PROTEIN MOTIFS

Program name Description
antigenic Finds antigenic sites in proteins
digest Reports on protein proteolytic enzyme or reagent cleavage sites
emast Motif detection
ememe Motif detection
epestfind Finds PEST motifs as potential proteolytic cleavage sites
fuzzpro Search for patterns in protein sequences
fuzztran Search for patterns in protein sequences (translated)
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
oddcomp Identify proteins with specified sequence word composition
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
preg Regular expression search of protein sequence(s)
pscan Scans protein sequence(s) with fingerprints from the PRINTS database
sigcleave Reports on signal cleavage sites in a protein sequence

PROTEIN MUTATION

Program name Description
msbar Mutate a sequence
shuffleseq Shuffles a set of sequences maintaining composition

PROTEIN PROFILES

Program name Description
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

UTILS DATABASE CREATION

Program name Description
aaindexextract Extract amino acid property data from AAINDEX
cutgextract Extract codon usage tables from from CUTG database
jaspextract Extract data from JASPAR
printsextract Extract data from PRINTS database for use by pscan
prosextract Processes the PROSITE motif database for use by patmatmotifs
rebaseextract Process the REBASE database for use by restriction enzyme applications
tfextract Process TRANSFAC transcription factor database for use by tfscan

UTILS DATABASE INDEXING

Program name Description
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

UTILS MISC

Program name Description
embossdata Find and retrieve EMBOSS data files
embossversion Writes the current EMBOSS version number to a file