The Software List

Program name	Source	Description
A	next	Back    Top
aacomp	FastA	Calculates the amino acid composition and molecular weight of a sequence.
acdc	EMBOSS	Tests definition files for any EMBOSS application.
align	FastA	Optimal global alignment of two sequences
align0	FastA	As align, but does not penalize for end-gaps.
antigenic	EMBOSS	Finds antigenic sites in proteins
Assemble	GCG	Combines fragments into one sequence
B	next	Back    Top
backtranseq	EMBOSS	Back translate a protein sequence
BackTranslate	GCG	Back translate a protein sequence
banana	EMBOSS	Bending and Curvature Plot in B-DNA
BestFit	GCG	Smith-Waterman local alignments
bestscor	FastA	Calculates the best self-comparison score.
BLAST	GCG	Blast on local databases
Breakup	GCG	Breaks large files into smaller overlapping ones
C	next	Back    Top
chaos	EMBOSS	Create a chaos plot for a sequence.
checktrans	EMBOSS	ORF property statistics
chips	EMBOSS	Codon usage statistics
Chopup	GCG	Converts very long lines in files to small ones
cirdna	EMBOSS	Draws circular maps of DNA constructs
clique	Phylip	Finds largest clique of mutually compatible characters.
clustalw	igmbc-fr	Multiple alignment program (command line based).
clustalx	igmbc-fr	Multiple alignment program (X-windows based).
cluster	EMBOSS	DNA sequence clustering
codcmp	EMBOSS	Codon usage table comparison
CodonFrequency	GCG	Tabulates the codon frequency in sequences
CodonPreference	GCG	Gene finder based on codon frequency
CoilScan	GCG	Finds coiled coil segments in proteins
Compare	GCG	Compares two sequences to make a file for DotPlot
complex	EMBOSS	Find the linguistic complexity in nucleotide sequences
Composition	GCG	Determines the nucleic/amino acid composition of sequences
CompressText	GCG	Removes "white space" from files
compseq	EMBOSS	Counts the composition of dimer/trimer/etc words in a sequence
CompTable	GCG	Create a (simplified) scoring matrix.
consense	Phylip	Computes majority-rule and strict consensus trees.
Consensus	GCG	Generates a consensus sequence for short nucleotide sequences.
contml	Phylip	Phylogenies from maximum likelihood on gene frequency data.
contrast	Phylip	Computes contrasts and correlations for comparative method studies.
Correspond	GCG	Compares patterns of codon usage.
Corrupt	GCG	Randomly introduce mutations into a nucleotide sequence.
cpgplot	EMBOSS	Plot CpG rich areas
cpgreport	EMBOSS	Reports CpG rich regions
crandseq	FastA	Produces a randomly shuffled DNA sequence keeping the codons intact.
cusp	EMBOSS	Create a codon usage table
cutseq	EMBOSS	Removes a specified section from a sequence.
D	next	Back    Top
dan	EMBOSS	Plot melting temperatures for DNA.
DataSet	GCG	Creates a GCG data library from GCG sequences
dbiblast	EMBOSS	Database indexing for BLAST 1 and 2 indexed databases
dbifasta	EMBOSS	Index a fasta database
dbiflat	EMBOSS	Database indexing for flat file databases
dbigcg	EMBOSS	Database indexing for GCG formatted databases
descseq	EMBOSS	Alter the name or description of a sequence.
Detab	GCG	Replaces tab characters with spaces.
diffseq	EMBOSS	Find differences (SNPs) between nearly identical sequences
digest	EMBOSS	Protein proteolytic enzyme or reagent cleavage digest
Distances	GCG	Creates a table of pair-wise distances from aligned sequences.
Diverge	GCG	Estimate the number of substitutions between two coding sequences.
dnacomp	Phylip	Phylogenies from DNA by the Compatibility criterion.
dnadist	Phylip	Computes four distance measures from nucleic acid sequences.
dnainvar	Phylip	Phylogenetic invariants method.
dnaml	Phylip	Phylogenies from DNA by maximum likelihood.
dnamlk	Phylip	Phylogenies from DNA by maximum likelihood with a molecular clock.
dnamove	Phylip	Interactive DNA phylogenies by parsimony or compatibility.
dnapars	Phylip	Nucleotide phylogenies by parsimony methods.
dnapenny	Phylip	DNA phylogenies by branch-and-bound.
dollop	Phylip	Phylogenies from the Dollo or polymorphism parsimony criteria.
dolmove	Phylip	Interactive construction of phylogenies using the Dollo or polymorphism parsimony criteria.
dolpenny	Phylip	Branch-and-bound phylogenies from the Dollo or polymorphism parsimony criteria.
dotmatcher	EMBOSS	Produces a dotplot of two sequences.
dotpath	EMBOSS	Displays a non-overlapping wordmatch dotplot of two sequences
DotPlot	GCG	Creates a dot plot using a file from Compare or StemLoop.
dottup	EMBOSS	DNA sequence dot plot
drawgram	Phylip	Draws cladograms and phenograms.
drawtree	Phylip	Draws unrooted phylogenies.
dreg	EMBOSS	Regular expression search of a nucleotide sequence
E	next	Back    Top
einverted	EMBOSS	Finds DNA inverted repeats
embossdata	EMBOSS	Finds or fetches the data files read in by the EMBOSS programs
emma	EMBOSS	Multiple alignment program
equicktandem	EMBOSS	Finds tandem repeats
est2genome	EMBOSS	Align EST and genomic DNA sequences
etandem	EMBOSS	Looks for tandem repeats in a nucleotide sequence.
extractseq	EMBOSS	Extract regions from a sequence.
ExtractPeptide	GCG	Writes a peptide sequence from a frame of Map.
F	next	Back    Top
factor	Phylip	Recodes multistate data to two state data.
FastA	GCG	FastA on local databases.
FastX	GCG	FastX on local databases.
Fetch	GCG	Get a sequence from a GCG database.
Figure	GCG	Makes figures from GCG program output.
findkm	EMBOSS	Calculates Km and Vmax for an enzyme reaction
FindPatterns	GCG	Searches for short patterns in sequences.
FingerPrint	GCG	Identifies products of T1 ribonuclease digestion.
fitch	Phylip	Phylogenies by the Fitch-Margoliash and least-squares methods.
FitConsensus	GCG	Finds matches to a consensus sequence matrix.
flalign	FastA	Plots lalign local alignments to a GCG Figure file.
FrameAlign	GCG	Local (or Global) alignment of a protein sequence to all frames of a nucleic acid sequence.
Frames	GCG	Translates in all six frames.
FrameSearch	GCG	Aligns groups of protein sequences to nucleotide sequence(s) in all frames.
freak	EMBOSS	Residue/base frequency table or plot
FromEMBL	GCG	Reformats an EMBL distribution file to GCG format.
FromFastA	GCG	Reformats FastA format files to GCG format.
fromgb	FastA	Convert from GenBank LOCUS format to Pearson/FASTA format.
FromGenBank	GCG	Reformats GenBank distribution files to GCG format.
FromIG	GCG	Reformats IntelliGenetics files to GCG format.
FromPIR	GCG	Reformat PIR format files to GCG format.
FromStaden	GCG	Reformat Staden format files to GCG format.
fuzznuc	EMBOSS	Nucleic acid pattern search
fuzzpro	EMBOSS	Protein pattern search
fuzztran	EMBOSS	Protein pattern search after translation
G	next	Back    Top
Gap	GCG	Needleman-Wunsch global alignment
gap4	Staden	Performs assembly, contig joining, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing.
Gapshow	GCG	Graphical representation of an alignment.
garnier	EMBOSS	Predicts protein secondary structure
garnier	FastA	Secondary structure prediction by the GOR method.
GCGtoBLAST	GCG	Combines GCG format sequences into a Blast searchable database.
geecee	EMBOSS	Calculates the fractional GC content of a nucleic acid sequence
GelAssemble	GCG	Multiple sequence editor for assembled contigs.
GelDisassemble	GCG	Breaks up contigs into single fragments.
GelEnter	GCG	Adds fragments to an assembly project.
GelMerge	GCG	Aligns sequence assembly fragments into contigs
GelStart	GCG	Starts a new fragment assembly project.
GelView	GCG	Displays structure of contigs in an assembly project.
gendist	Phylip	Computes three genetic distances from gene frequency data.
getorf	EMBOSS	Finds and extracts open reading frames (ORFs)
GetSeq	GCG	Create a sequence file from a terminal.
grease	FastA	Kyte-Doolittle hydropathicity profile
GrowTree	GCG	Generates a tree from a distance matrix.
H	next	Back    Top
HelicalWheel	GCG	Plots a peptide sequence as a helical wheel.
helixturnhelix	EMBOSS	Finds nucleic acid binding domains.
HTHScan	GCG	Searches for helix-turn-helix motifs.
I	next	Back    Top
iep	EMBOSS	Calculates the isoelectric point of a protein
infoseq	EMBOSS	Displays some simple information about sequences
isochore	EMBOSS	Plots isochores in large DNA sequences
Isoelectric	GCG	Plots charge as a function of pH for a peptide sequence.
J	next	Back    Top
K	next	Back    Top
kitsch	Phylip	Phylogenies by the Fitch-Margoliash and least-squares methods with a molecular clock.
L	next	Back    Top
lalign	FastA	Local sequence alignment program that displays the N-best local alignments.
lfasta	FastA	local similarity searches showing local alignments.
lindna	EMBOSS	Draws linear maps of DNA constructs
LineUp	GCG	Editor for multiple alignments.
ListFile	GCG	Print a file on a terminals by pass port.
LookUp	GCG	Find a sequence data base entry by SRS.
LPrint	GCG	Prints a PostScript file.
M	next	Back    Top
Map	GCG	Find restriction enzyme sites.
MapPlot	GCG	Displays restriction enzyme sites graphically.
MapSort	GCG	Sorts restriction enzyme digest fragments by size.
maskseq	EMBOSS	Mask off regions of a sequence.
matcher	EMBOSS	Local alignment of two sequences
megamerger	EMBOSS	Merge two large overlapping nucleic acid sequences
MEME	GCG	Finds conserved motifs in a group of unaligned sequences.
merger	EMBOSS	Merge two overlapping sequences
MFold	GCG	Predicts optimal secondary structure in nucleotide sequences.
mix	Phylip	Wagner, Camin-Sokal and mixed parsimony methods.
Moment	GCG	Makes a contour plot of the helical hydrophobic moment of a peptide sequence.
Motifs	GCG	Searches for ProSite patterns in a sequence.
MotifSearch	GCG	Searches a set of sequences with a profile.
move	Phylip	Interactive construction of phylogenies from two-state data.
msbar	EMBOSS	Mutate sequence beyond all recognition
N	next	Back    Top
Name	GCG	Change GCG logical names.
Names	GCG	Identifies GCG data files and sequence entries by name
needle	EMBOSS	Needleman-Wunsch global alignment.
neighbor	Phylip	Neighbour-joining and UPGMA methods.
NetBLAST	GCG	Blast search at NCBI.
NetFetch	GCG	Interface to NetEntrez to get sequences from NetBlast search.
newcpgreport	EMBOSS	Report CpG rich areas
newcpgseek	EMBOSS	Reports CpG rich regions
newseq	EMBOSS	Type in a short new sequence.
nip4	Staden	Analyses nucleotide sequences to find genes, restriction sites and motifs. It will perform translations, find ORFs and examine codon usage.
NoOverlap	GCG	Identifies where a group of nucleotide sequences have no common subsequences.
noreturn	EMBOSS	Removes carriage return from ASCII files
nthseq	EMBOSS	Writes one sequence from a multiple set of sequences
O	next	Back    Top
octanol	EMBOSS	Displays protein hydropathy
oddcomp	EMBOSS	Finds protein sequence regions with a biased composition.
OldDistances	GCG	Makes a table of pairwise similarities from aligned sequences.
OneCase	GCG	Changes the case of the letters in a file.
Overlap	GCG	Looks for overlaps in a set of sequences.
P	next	Back    Top
palindrome	EMBOSS	Looks for inverted repeats in a nucleotide sequence.
pasteseq	EMBOSS	Insert one sequence into another.
patmatdb	EMBOSS	Matching a Prosite motif against a Protein Sequence Database.
patmatmotifs	EMBOSS	Compares a protein sequence to the PROSITE motif database.
PAUPDisplay	GCG	An interface to tree manipulation, diagnosis, and display options in PAUP
PAUPSearch	GCG	An interface to the tree-searching options in PAUP
penny	Phylip	Finds all most parsimonious trees by branch-and-bound.
pepcoil	EMBOSS	Predicts coiled coil regions
PepData	GCG	Translates in six frames and concatenates peptide sequences
pepinfo	EMBOSS	Plots simple amino acid properties in parallel
pepnet	EMBOSS	Protein helical net plot
PepPlot	GCG	Plots measures of protein secondary structure and hydrophobicity
pepstats	EMBOSS	Protein statistics such as isoelectric point and molecular weight
PeptideMap	GCG	Marks a peptide sequence where a known proteolytic agent might cut it.
Peptidesort	GCG	Orders the fragments from a digest of an amino acid sequence.
PeptideStructure	GCG	Secondary structure and related predictions for a peptide sequence.
pepwheel	EMBOSS	Protein helical wheel plot
pepwindow	EMBOSS	Displays protein hydropathy
pepwindowall	EMBOSS	Displays protein hydropathy of a set of sequences
PileUp	GCG	Multiple sequence alignment from progressive (tree based), pairwise alignments
plalign	FastA	Plots lalign local alignments to a postscript file.
PlasmidMap	GCG	Draws a circular plot of a plasmid construct.
plotorf	EMBOSS	Plot potential open reading frames
Plotsimilarity	GCG	Plots a running average of similarity among sequences in a multiple alignment.
PlotStructure	GCG	Plots the measures of protein secondary structure from PeptideStructure.
PlotTest	GCG	Plots an example graphic to test your graphics configuration.
polydot	EMBOSS	Multiple dotplot
prdf2	FastA	Calculates the probability of a similarity score using an extreme value distribution.
preg	EMBOSS	Regular expression search of a protein sequence
pregap4	Staden	Prepares sequence trace data for analysis or assembly.
Pretty	GCG	Displays multiple sequence alignments and calculates a consensus sequence.
PrettyBox	GCG	Displays multiple sequence alignments in PostScript format, using shading.
prettyplot	EMBOSS	Displays aligned sequences, with colouring and boxing.
prettyseq	EMBOSS	Output sequence with translated ranges
prima	EMBOSS	Selecting primers for PCR and DNA amplification.
Prime	GCG	Selects oligonucleotide primers for a template DNA sequence.
primersearch	EMBOSS	Searches DNA sequences for matches with primer pairs
printsextract	EMBOSS	Preprocesses the PRINTS database for use with the program PSCAN
ProfileGap	GCG	Makes an optimal alignment between a profile and one or more sequences.
ProfileMake	GCG	Creates a position-specific scoring table or profile.
ProfileScan	GCG	Finds motifs in a database of profiles.
ProfileSearch	GCG	Uses a profile to search a database.
ProfileSegments	GCG	Makes optimal alignments from similar segments found by ProfileSearch.
profit	EMBOSS	Scan a sequence or database with a matrix or profile
prophecy	EMBOSS	Creates matrices/profiles from multiple alignments
prophet	EMBOSS	Gapped alignment for profiles
prosextract	EMBOSS	Extracts ID, AC, and PA lines from the PROSITE motif database.
protdist	Phylip	Compute distance measures from protein sequences.
protpars	Phylip	Phylogenies by protein parsimony.
prss3	FastA	Evaluates the significance of pairwise similarity scores using a Monte Carlo analysis.
pscan	EMBOSS	Locates fingerprints (multiple motif features) in a protein sequence.
Publish	GCG	Arranges sequences for publication.
Q	next	Back    Top
R	next	Back    Top
randseq	FastA	Produces a randomly shuffled sequence from a query sequence.
Readseq	D. Gilbert	General sequence reformatting tool.
rebaseextract	EMBOSS	Extract data from REBASE
Red	GCG	A text formatter that creates publication-quality documents for a PostScript printer
redata	EMBOSS	Isoschizomers, references and Suppliers for Restriction Enzymes
Reformat	GCG	Rewrites sequence, scoring matrix, or enzyme data file(s) in GCG format.
remap	EMBOSS	Display a sequence with restriction cut sites, translation etc..
Repeat	GCG	Finds direct repeats in sequences.
Replace	GCG	Makes character string replacements in text file(s).
restml	Phylip	Phylogenies by maximum likelihood from restriction enzyme data.
restrict	EMBOSS	Finds Restriction Enzyme Cleavage Sites
retree	Phylip	Reroot, flip branches and change species names and branch lengths.
Reverse	GCG	Reverses and/or complements a sequence.
revseq	EMBOSS	Reverse and complement a sequence.
S	next	Back    Top
Sample	GCG	Extracts sequence fragments randomly from sequence(s).
seealso	EMBOSS	Finds programs sharing group names
Seg	GCG	Replaces low complexity regions in protein sequences with X characters.
Segments	GCG	Aligns and displays the segments of similarity found by WordSearch.
seqboot	Phylip	Bootstrap, jack-knife or permutation resampling analyses.
SeqEd	GCG	An interactive editor for entering and modifying sequences
SeqLab	GCG	The graphical user interface (X-windows) for the GCG Package.
seqmatchall	EMBOSS	All against all word based sequence comparison
seqret	EMBOSS	Reads and writes (returns) a sequence.
seqretall	EMBOSS	Reads and writes (returns) a set of sequences one at a time.
seqretset	EMBOSS	Reads and writes (returns) a set of sequences all at once.
SetKeys	GCG	Redefines your keyboard's keys for easier sequence entry in GCG programs.
SetPlot	GCG	Lists graphic devices available to the GCG programs.
ShiftOver	GCG	Moves a file to the right or left a few columns.
showdb	EMBOSS	Displays information on the currently available databases
showfeat	EMBOSS	Show features of a sequence.
showorf	EMBOSS	Pretty output of DNA translations
showseq	EMBOSS	Display a sequence with features, translation etc
Shuffle	GCG	Randomizes the order of a sequence without changing the composition.
shuffleseq	EMBOSS	Shuffles a set of sequences maintaining composition
sigcleave	EMBOSS	Predicts signal peptide cleavage sites.
Simplify	GCG	Reduces the number of symbols in a sequence based on similar properties.
sip4	Staden	Compares pairs of sequences. It includes dot plots, finding matching words, global and local optimal alignments and statistical evaluation of matches.
Spew	GCG	sends a GCG sequence to a personal computer acting as a terminal.
splitter	EMBOSS	Split a sequence into (overlapping) smaller sequences.
SPScan	GCG	Looks for the presence of secretory signal peptides.
SSearch	GCG	Smith-Waterman search of local GCG databases.
StatPlot	GCG	Plots a set of graphs from a table of numbers (eg from Window).
Stemloop	GCG	Finds stems (inverted repeats) within a sequence.
stretcher	EMBOSS	Global alignment of two sequences.
StringSearch	GCG	Identifies sequences by character patterns in the sequence documentation.
stssearch	EMBOSS	Searches a DNA sequence database with a set of STS primers and reports expected matches and possible mismatches. A replacement for stssearch in the EGCG package.
supermatcher	EMBOSS	Finds a match of one sequence against one or more sequences (for Large Sequences)
syco	EMBOSS	Synonymous codon usage Gribskov statistic plot
Symbol	GCG	Creates, changes, deletes, or displays GCG symbol(s) in the GCG symbol table.
T	next	Back    Top
Terminator	GCG	Searches for prokaryotic factor-independent RNA polymerase terminators.
TestCode	GCG	Identify potential protein coding regions by non-random third base composition.
textsearch	EMBOSS	Search sequence documentation text. SRS and Entrez are faster!
TFastA	GCG	TFasta on local (translated nucleotide) GCG databases.
TFastX	GCG	As TFasta but allowing for frame shifts.
tfextract	EMBOSS	Extract data from TRANSFAC
tfm	EMBOSS	Displays a program's help documentation manual
tfscan	EMBOSS	Scans DNA sequences for transcription factors.
tgrease	FastA	Graphic plot of Kyte-Doolittle hydropathicity profile.
tmap	EMBOSS	Predict transmembrane proteins
ToFastA	GCG	Converts GCG sequence(s) into FastA format.
ToIG	GCG	Converts GCG sequence file(s) into a single file in IntelliGenetics format.
ToPIR	GCG	Writes GCG sequence(s) into a single file in PIR format.
ToStaden	GCG	Writes a GCG sequence into a file in Staden format.
transeq	EMBOSS	Translates nucleic acid sequences.
Translate	GCG	Translates nucleotide sequences into peptide sequences.
trev	Staden	Allows viewing and editing of ABI, ALF or SCF trace files.
trimseq	EMBOSS	Trim ambiguous bits off the ends of sequences
U	next	Back    Top
V	next	Back    Top
vectorstrip	EMBOSS	Strips out DNA between a pair of vector sequences
W	next	Back    Top
water	EMBOSS	Smith-Waterman local alignment.
Window	GCG	Makes a table of the frequencies of sequence patterns within a window along a sequence.
wobble	EMBOSS	Wobble base plot
wordcount	EMBOSS	Counts words of a specified size in a DNA sequence.
wordmatch	EMBOSS	Finds all exact matches of a given size between 2 DNA sequences
WordSearch	GCG	Identifies sequences in a database by matching large numbers of words.
wossname	EMBOSS	Finds programs by keywords in their one-line documentation.
X	next	Back    Top
Xnu	GCG	Masks tandem repeats in protein sequences with X characters.
Y	next	Back    Top
Z	next	Back    Top
zs_exp	FastA	Converts a z-score (mean 50, s.d. 10) into an expectation value using the extreme value distribution and the size of the database

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