EMBOSS is a new, free open source software analysis package specially developed for the needs of the molecular biology community produced.  For details see EMBOSS.

Program name	Description
abiview	Reads ABI file and display the trace
acdc	Tests definition files for any EMBOSS application.
antigenic	Finds antigenic sites in proteins
backtranseq	Back translate a protein sequence
banana	Bending and Curvature Plot in B-DNA
btwisted	Calculates the twisting in a B-DNA sequence
cai	CAI codon usage statistic
chaos	Create a chaos plot for a sequence.
charge	Protein charge plot
checktrans	ORF property statistics
chips	Codon usage statistics
cirdna	Draws circular maps of DNA constructs
codcmp	Codon usage table comparison
coderet	Extract CDS, mRNA and translations from feature tables
compseq	Counts the composition of dimer/trimer/etc words in a sequence
contacts	Reads coordinate files and writes contact files
cons	Creates a consensus from multiple alignments
cpgplot	Plot CpG rich areas
cpgreport	Reports CpG rich regions
cusp	Create a codon usage table
cutseq	Removes a specified section from a sequence.
dan	Plot melting temperatures for DNA.
dbiblast	Database indexing for BLAST 1 and 2 indexed databases
dbifasta	Index a fasta database
dbiflat	Database indexing for flat file databases
dbigcg	Database indexing for GCG formatted databases
degapseq	Removes gap characters from sequences
descseq	Alter the name or description of a sequence.
diffseq	Find differences (SNPs) between nearly identical sequences
digest	Protein proteolytic enzyme or reagent cleavage digest
distmat	Creates a distance matrix from multiple alignments
domainer	Build domain coordinate files
dotmatcher	Produces a dotplot of two sequences.
dotpath	Displays a non-overlapping wordmatch dotplot of two sequences
dottup	DNA sequence dot plot
dreg	Regular expression search of a nucleotide sequence
einverted	Finds DNA inverted repeats
embossdata	Finds or fetches the data files read in by the EMBOSS programs
embossversion	Writes the current EMBOSS version number
emowse	Protein identification by mass spectrometry
emma	Multiple alignment program
entret	Reads and writes (returns) flatfile entries
equicktandem	Finds tandem repeats
est2genome	Align EST and genomic DNA sequences
etandem	Looks for tandem repeats in a nucleotide sequence.
extractseq	Extract regions from a sequence.
findkm	Calculates Km and Vmax for an enzyme reaction
freak	Residue/base frequency table or plot
fuzznuc	Nucleic acid pattern search
fuzzpro	Protein pattern search
fuzztran	Protein pattern search after translation
garnier	Predicts protein secondary structure
geecee	Calculates the fractional GC content of nucleic acid sequences
getorf	Finds and extracts open reading frames (ORFs)
helixturnhelix	Finds nucleic acid binding domains.
hmoment	Hydrophobic moment calculation
iep	Calculates the isoelectric point of a protein
infoalign	Information on a multiple sequence alignment
infoseq	Displays some simple information about sequences
isochore	Plots isochores in large DNA sequences
lindna	Draws linear maps of DNA constructs
marscan	Finds MAR/SAR sites in nucleic sequences
maskfeat	Mask off features of a sequence
maskseq	Mask off regions of a sequence.
matcher	Local alignment of two sequences
megamerger	Merge two large overlapping nucleic acid sequences
merger	Merge two overlapping sequences
msbar	Mutate sequence beyond all recognition
needle	Needleman-Wunsch global alignment.
newcpgreport	Report CpG rich areas
newcpgseek	Reports CpG rich regions
newseq	Type in a short new sequence.
noreturn	Removes carriage return from ASCII files
notseq	Excludes a set of sequences and writes out the remaining ones
nrscope	Converts redundant EMBL-format SCOP file to non-redundant one
nthseq	Writes one sequence from a multiple set of sequences
octanol	Displays protein hydropathy
oddcomp	Finds protein sequence regions with a biased composition.
palindrome	Looks for inverted repeats in a nucleotide sequence.
pasteseq	Insert one sequence into another.
patmatdb	Matching a Prosite motif against a Protein Sequence Database.
patmatmotifs	Compares a protein sequence to the PROSITE motif database.
pepcoil	Predicts coiled coil regions
pepinfo	Plots simple amino acid properties in parallel
pepnet	Protein helical net plot
pepstats	Protein statistics
pepwheel	Shows protein sequences as helices
pepwindow	Displays protein hydropathy
pepwindowall	Displays protein hydropathy of a set of sequences
plotcon	Plots the quality of conservation of a sequence alignment
plotorf	Plot potential open reading frames
polydot	Multiple dotplot
preg	Regular expression search of a protein sequence
prettyplot	Displays aligned sequences, with colouring and boxing.
prettyseq	Output sequence with translated ranges
prima	Selecting primers for PCR and DNA amplification.
primersearch	Searches DNA sequences for matches with primer pairs
printsextract	Preprocesses the PRINTS database for use with the program PSCAN
profit	Scan a sequence or database with a matrix or profile
prophecy	Creates matrices/profiles from multiple alignments
prophet	Gapped alignment for profiles
prosextract	Extracts ID, AC, and PA lines from the PROSITE motif database.
pscan	Locates fingerprints (multiple motif features) in a protein sequence.
rebaseextract	Extract data from REBASE
recoder	Find and remove restriction sites but maintain the same translation
redata	Isoschizomers, references and Suppliers for Restriction Enzymes
remap	Display a sequence with restriction cut sites, translation etc..
restover	Finds restriction enzymes that produce a specific overhang
restrict	Finds Restriction Enzyme Cleavage Sites
revseq	Reverse and complement a sequence.
scopalign	Generate alignments for SCOP families
scope	Convert raw scop classification file to embl-like format
seealso	Finds programs sharing group names
seqmatchall	Does an all-against-all comparison of a set of sequences
seqret	Reads and writes (returns) a sequence.
seqretall	Reads and writes (returns) a set of sequences one at a time.
seqretallfeat	Reads and writes (returns) one or more sequences
seqretset	Reads and writes (returns) a set of sequences all at once.
seqretsplit	Reads and writes (returns) sequences in individual files
showdb	Displays information on the currently available databases
showalign	Display a multiple sequence alignment
showfeat	Show features of a sequence.
showorf	Pretty output of DNA translations
showseq	Display a sequence with features, translation etc
shuffleseq	Shuffles a set of sequences maintaining composition
sigcleave	Predicts signal peptide cleavage sites
siggen	Generates a sparse protein signature
sigscan	Scans a sparse protein signature against swissprot
silent	Silent mutation restriction enzyme scan
splitter	Split a sequence into (overlapping) smaller sequences.
stamps	Generate alignments for SCOP families
stretcher	Global alignment of two sequences.
stssearch	Searches a DNA database for matches with a set of STS primers
supermatcher	Finds a match of a large sequence against one or more sequences
syco	Synonymous codon usage Gribskov statistic plot
textsearch	Search sequence documentation text. SRS and Entrez are faster!
tfextract	Extract data from TRANSFAC
tfm	Displays a program's help documentation manual
tfscan	Scans DNA sequences for transcription factors.
tmap	Predict transmembrane proteins
transeq	Translates nucleic acid sequences.
trimseq	Trim ambiguous bits off the ends of sequences
vectorstrip	Strips out DNA between a pair of vector sequences
water	Smith-Waterman local alignment.
wobble	Wobble base plot
wordcount	Counts words of a specified size in a DNA sequence.
wordmatch	Finds all exact matches of a given size between 2 sequences
wossname	Finds programs by keywords in their one-line documentation.