Difference between revisions of "List of EMBOSS programs"

Revision as of 07:32, 7 September 2007 (view source) Christoph (Talk | contribs) (→‎Publication-quality display) ← Older edit		Latest revision as of 01:04, 10 July 2012 (view source) Christoph (Talk | contribs)
Line 445:		Line 445:
	;embossdata : Finds or fetches data files read by EMBOSS programs		;embossdata : Finds or fetches data files read by EMBOSS programs
	;embossversion : Writes the current EMBOSS version number		;embossversion : Writes the current EMBOSS version number
		+
		+	==External / contributed packages==
		+	;CBSTOOLS: The CBSTOOLS package is a set of wrappers to selected applications from the [http://cbs.dtu.dk/ CBS group] in Denmark.
		+
		+	;CLUSTALOMEGA: A wrapper for the clustal omega application.
		+
		+	;DOMAINATRIX: The DOMAINATRIX programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.
		+
		+	;DOMALIGN: The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.
		+
		+	;DOMSEARCH: The DOMSEARCH programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.
		+
		+	;EMBOSS: The latest stable version of EMBOSS (excluding bugfix patches from the 'fixes' directory hierarchy)
		+
		+	;EMNU: The EMNU package is a simple EMBOSS menu system written by Gary Williams at HGMP.
		+
		+	;ESIM4: The ESIM4 package is an EMBOSS conversion of the SIM4 package from Liliana Florea.
		+
		+	;HMMER: A suite of application wrappers to the original hmmer v2.3.2 applications written by Sean Eddy. hmmer v2.3.2 must be installed on the same system as EMBOSS and the location of the hmmer executables must be defined in your path for EMBASSY HMMER to work.
		+
		+	;IPRSCAN: The IPRSCAN package is a wrapper for the interproscan program.
		+
		+	;MEME: The EMBASSY MEME package contains 'wrapper' applications providing an EMBOSS-style interface to the applications in the original MEME package version 4.0.0 developed by Timothy L. Bailey.
		+
		+	;MIRA: The MIRA package is a fragment assembly program from Bastien Chevreux. The program was converted to EMBOSS by Alan Bleasby as two applications, one for EST assembly and one for shotgun fragment assembly
		+
		+	;MSE: The MSE package is a multiple sequence editor. The program was contributed to the EMBOSS package by the author, Will Gilbert, as one of the first EMBASSY programs.
		+
		+	;MYEMBOSS: A package for your own software developments.
		+
		+	;MYEMBOSSDEMO: The MYEMBOSSDEMO package contains example applications using EMBOSS data types
		+
		+	;PHYLIPNEW: The PHYLIPNEW programs are EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, version 3.69.
		+
		+	;SIGNATURE: The SIGNATURE programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.
		+
		+	;STRUCTURE: The STRUCTURE programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.
		+
		+	;TOPO: The TOPO package is a graphics program to display membrane protein topology by Susan Jean Johns.
		+
		+	;VIENNA: These programs are adapted from the VIENNA RNA package.
	[[Category:EMBOSS| ]]		[[Category:EMBOSS| ]]

---

Latest revision as of 01:04, 10 July 2012

Acd file utilities

acdc 

ACD compiler

acdpretty 

ACD pretty printing utility

acdtable 

Creates an HTML table from an ACD file

acdtrace 

ACD compiler on-screen trace

acdvalid 

ACD file validation

Merging sequences to make a consensus

cons 

Creates a consensus from multiple alignments

megamerger 

Merge two large overlapping nucleic acid sequences

merger 

Merge two overlapping sequences

Finding differences between sequences

diffseq 

Find differences between nearly identical sequences

Dot plot sequence comparisons

dotmatcher 

Displays a thresholded dotplot of two sequences

dotpath 

Non-overlapping wordmatch dotplot of two sequences

dottup 

Displays a wordmatch dotplot of two sequences

polydot 

Displays all-against-all dotplots of a set of sequences

Global sequence alignment

est2genome 

Align EST and genomic DNA sequences

needle 

Needleman-Wunsch global alignment

stretcher 

Finds the best global alignment between two sequences

esim4 

Align an mRNA to a genomic DNA sequence

Local sequence alignment

matcher 

Finds the best local alignments between two sequences

seqmatchall 

All-against-all comparison of a set of sequences

supermatcher 

Match large sequences against one or more other sequences

water 

Smith-Waterman local alignment

wordfinder 

Match large sequences against one or more other sequences

wordmatch 

Finds all exact matches of a given size between 2 sequences

Multiple sequence alignment

edialign 

Local multiple alignment of sequences

emma 

Multiple alignment program - interface to ClustalW program

infoalign 

Information on a multiple sequence alignment

plotcon 

Plot quality of conservation of a sequence alignment

prettyplot 

Displays aligned sequences, with colouring and boxing

showalign 

Displays a multiple sequence alignment

tranalign 

Align nucleic coding regions given the aligned proteins

mse 

Multiple Sequence Editor

Publication-quality display

abiview 

Reads ABI file and display the trace

cirdna 

Draws circular maps of DNA constructs

lindna 

Draws linear maps of DNA constructs

pepnet 

Displays proteins as a helical net

pepwheel 

Shows protein sequences as helices

prettyplot 

Displays aligned sequences, with colouring and boxing

prettyseq 

Output sequence with translated ranges

remap 

Display sequence with restriction sites, translation etc

seealso 

Finds programs sharing group names

showalign 

Displays a multiple sequence alignment

showdb 

Displays information on the currently available databases

showfeat 

Show features of a sequence

showseq 

Display a sequence with features, translation etc

sixpack 

Display a DNA sequence with 6-frame translation and ORFs

textsearch 

Search sequence documentation. Slow, use SRS and Entrez!

Enzyme kinetics calculations

findkm 

Find Km and Vmax for an enzyme reaction

Manipulation and display of sequence annotation

coderet 

Extract CDS, mRNA and translations from feature tables

extractfeat 

Extract features from a sequence

maskfeat 

Mask off features of a sequence

showfeat 

Show features of a sequence

twofeat 

Finds neighbouring pairs of features in sequences

Hidden markov model analysis

oalistat 

Statistics for multiple alignment files

ohmmalign 

Align sequences with an HMM

ohmmbuild 

Build HMM

ohmmcalibrate 

Calibrate a hidden Markov model

ohmmconvert 

Convert between HMM formats

ohmmemit 

Extract HMM sequences

ohmmfetch 

Extract HMM from a database

ohmmindex 

Index an HMM database

ohmmpfam 

Align single sequence with an HMM

ohmmsearch 

Search sequence database with an HMM

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 and general help for users

infoalign 

Information on a multiple sequence alignment

infoseq 

Displays some simple information about sequences

seealso 

Finds programs sharing group names

showdb 

Displays information on the currently available databases

textsearch 

Search sequence documentation. Slow, use SRS and Entrez!

tfm 

Displays a program's help documentation manual

whichdb 

Search all databases for an entry

wossname 

Finds programs by keywords in their one-line documentation

Menu interface(s)

emnu 

Simple menu of EMBOSS applications

Nucleic acid secondary structure

einverted 

Finds DNA inverted repeats

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

Codon usage analysis

cai 

CAI codon adaptation index

chips 

Codon usage statistics

codcmp 

Codon usage table comparison

cusp 

Create a codon usage table

syco 

Synonymous codon usage Gribskov statistic plot

Composition of nucleotide sequences

banana 

Bending and curvature plot in B-DNA

btwisted 

Calculates the twisting in a B-DNA sequence

chaos 

Create a chaos game representation plot for a sequence

compseq 

Count composition of dimer/trimer/etc words in a sequence

dan 

Calculates DNA RNA/DNA melting temperature

freak 

Residue/base frequency table or plot

isochore 

Plots isochores in large DNA sequences

sirna 

Finds siRNA duplexes in mRNA

wordcount 

Counts words of a specified size in a DNA sequence

CpG island detection and analysis

cpgplot 

Plot CpG rich areas

cpgreport 

Reports all CpG rich regions

geecee 

Calculates fractional GC content of nucleic acid sequences

newcpgreport 

Report CpG rich areas

newcpgseek 

Reports CpG rich regions

Predictions of genes and other genomic features

getorf 

Finds and extracts open reading frames (ORFs)

marscan 

Finds MAR/SAR sites in nucleic sequences

plotorf 

Plot potential open reading frames

showorf 

Pretty output of DNA translations

sixpack 

Display a DNA sequence with 6-frame translation and ORFs

syco 

Synonymous codon usage Gribskov statistic plot

tcode 

Fickett TESTCODE statistic to identify protein-coding DNA

wobble 

Wobble base plot

Nucleic acid motif searches

dreg 

Regular expression search of a nucleotide sequence

fuzznuc 

Nucleic acid pattern search

fuzztran 

Protein pattern search after translation

marscan 

Finds MAR/SAR sites in nucleic sequences

Nucleic acid sequence mutation

msbar 

Mutate sequence beyond all recognition

shuffleseq 

Shuffles a set of sequences maintaining composition

Primer prediction

eprimer3 

Picks PCR primers and hybridization oligos

primersearch 

Searches DNA sequences for matches with primer pairs

stssearch 

Search a DNA database for matches with a set of STS primers

Nucleic acid profile generation and searching

profit 

Scan a sequence or database with a matrix or profile

prophecy 

Creates matrices/profiles from multiple alignments

prophet 

Gapped alignment for profiles

Nucleic acid repeat detection

einverted 

Finds DNA inverted repeats

equicktandem 

Finds tandem repeats

etandem 

Looks for tandem repeats in a nucleotide sequence

palindrome 

Looks for inverted repeats in a nucleotide sequence

Restriction enzyme sites in nucleotide sequences

recoder 

Remove restriction sites but maintain same translation

redata 

Search REBASE for enzyme name, references, suppliers etc

remap 

Display sequence with restriction sites, translation etc

restover 

Find restriction enzymes producing specific overhang

restrict 

Finds restriction enzyme cleavage sites

showseq 

Display a sequence with features, translation etc

silent 

Silent mutation restriction enzyme scan

Transcription factors, promoters and terminator prediction

tfscan 

Scans DNA sequences for transcription factors

Translation of nucleotide sequence to protein sequence

backtranambig 

Back translate a protein sequence to ambiguous codons

backtranseq 

Back translate a protein sequence

coderet 

Extract CDS, mRNA and translations from feature tables

plotorf 

Plot potential open reading frames

prettyseq 

Output sequence with translated ranges

remap 

Display sequence with restriction sites, translation etc

showorf 

Pretty output of DNA translations

showseq 

Display a sequence with features, translation etc

sixpack 

Display a DNA sequence with 6-frame translation and ORFs

transeq 

Translate nucleic acid sequences

Phylogenetic consensus methods

econsense 

Majority-rule and strict consensus tree

fconsense 

Majority-rule and strict consensus tree

ftreedist 

Distances between trees

ftreedistpair 

Distances between two sets of trees

Phylogenetic continuous character methods

econtml 

Continuous character Maximum Likelihood method

econtrast 

Continuous character Contrasts

fcontrast 

Continuous character Contrasts

Phylogenetic discrete character methods

eclique 

Largest clique program

edollop 

Dollo and polymorphism parsimony algorithm

edolpenny 

Penny algorithm Dollo or polymorphism

efactor 

Multistate to binary recoding program

emix 

Mixed parsimony algorithm

epenny 

Penny algorithm, branch-and-bound

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

Phylogenetic distance matrix methods

efitch 

Fitch-Margoliash and Least-Squares Distance Methods

ekitsch 

Fitch-Margoliash method with contemporary tips

eneighbor 

Phylogenies from distance matrix by N-J or UPGMA method

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

Phylogenetic gene frequency methods

egendist 

Genetic Distance Matrix program

fcontml 

Gene frequency and continuous character Maximum Likelihood

fgendist 

Compute genetic distances from gene frequencies

Phylogenetic tree drawing methods

distmat 

Creates a distance matrix from multiple alignments

ednacomp 

DNA compatibility algorithm

ednadist 

Nucleic acid sequence Distance Matrix program

ednainvar 

Nucleic acid sequence Invariants method

ednaml 

Phylogenies from nucleic acid Maximum Likelihood

ednamlk 

Phylogenies from nucleic acid Maximum Likelihood with clock

ednapars 

DNA parsimony algorithm

ednapenny 

Penny algorithm for DNA

eprotdist 

Protein distance algorithm

eprotpars 

Protein parsimony algorithm

erestml 

Restriction site Maximum Likelihood method

eseqboot 

Bootstrapped sequences algorithm

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

Phylogenetic molecular sequence methods

fdrawgram 

Plots a cladogram- or phenogram-like rooted tree diagram

fdrawtree 

Plots an unrooted tree diagram

fretree 

Interactive tree rearrangement

Protein secondary structure

garnier 

Predicts protein secondary structure

helixturnhelix 

Report nucleic acid binding motifs

hmoment 

Hydrophobic moment calculation

pepcoil 

Predicts coiled coil regions

pepnet 

Displays proteins as a helical net

pepwheel 

Shows protein sequences as helices

tmap 

Displays membrane spanning regions

topo 

Draws an image of a transmembrane protein

Protein tertiary structure

psiphi 

Phi and psi torsion angles from protein coordinates

domainreso 

Remove low resolution domains from a DCF file

domainalign 

Generate alignments (DAF file) for nodes in a DCF file

domainrep 

Reorder DCF file to identify representative structures

seqalign 

Extend alignments (DAF file) with sequences (DHF file)

seqfraggle 

Removes fragment sequences from DHF files

seqsearch 

Generate PSI-BLAST hits (DHF file) from a DAF file

seqsort 

Remove ambiguous classified sequences from DHF files

seqwords 

Generates DHF files from keyword search of UniProt

libgen 

Generate discriminating elements from alignments

matgen3d 

Generate a 3D-1D scoring matrix from CCF files

rocon 

Generates a hits file from comparing two DHF files

rocplot 

Performs ROC analysis on hits files

siggen 

Generates a sparse protein signature from an alignment

siggenlig 

Generate ligand-binding signatures from a CON file

sigscan 

Generate hits (DHF file) from a signature search

sigscanlig 

Search ligand-signature library & write hits (LHF file)

contacts 

Generate intra-chain CON files from CCF files

interface 

Generate inter-chain CON files from CCF files

Composition of protein sequences

backtranambig 

Back translate a protein sequence to ambiguous codons

backtranseq 

Back translate a protein sequence

charge 

Protein charge plot

checktrans 

Reports STOP codons and ORF statistics of a protein

compseq 

Count composition of dimer/trimer/etc words in a sequence

emowse 

Protein identification by mass spectrometry

freak 

Residue/base frequency table or plot

iep 

Calculates the isoelectric point of a protein

mwcontam 

Shows molwts that match across a set of files

mwfilter 

Filter noisy molwts from mass spec output

octanol 

Displays protein hydropathy

pepinfo 

Plots simple amino acid properties in parallel

pepstats 

Protein statistics

pepwindow 

Displays protein hydropathy

pepwindowall 

Displays protein hydropathy of a set of sequences

Protein motif searches

antigenic 

Finds antigenic sites in proteins

digest 

Protein proteolytic enzyme or reagent cleavage digest

epestfind 

Finds PEST motifs as potential proteolytic cleavage sites

fuzzpro 

Protein pattern search

fuzztran 

Protein pattern search after translation

helixturnhelix 

Report nucleic acid binding motifs

oddcomp 

Find protein sequence regions with a biased composition

patmatdb 

Search a protein sequence with a motif

patmatmotifs 

Search a PROSITE motif database with a protein sequence

pepcoil 

Predicts coiled coil regions

preg 

Regular expression search of a protein sequence

pscan 

Scans proteins using PRINTS

sigcleave 

Reports protein signal cleavage sites

omeme 

Motif detection

emast 

Motif detection

ememe 

Motif detection

Protein sequence mutation

msbar 

Mutate sequence beyond all recognition

shuffleseq 

Shuffles a set of sequences maintaining composition

Protein profile generation and searching

profit 

Scan a sequence or database with a matrix or profile

prophecy 

Creates matrices/profiles from multiple alignments

prophet 

Gapped alignment for profiles

Testing tools, not for general use

crystalball 

Answers every drug discovery question about a sequence

myseq 

Demonstration of sequence reading

mytest 

Demonstration of sequence reading

Database installation

aaindexextract 

Extract data from AAINDEX

cutgextract 

Extract data from CUTG

printsextract 

Extract data from PRINTS

prosextract 

Build the PROSITE motif database for use by patmatmotifs

rebaseextract 

Extract data from REBASE

tfextract 

Extract data from TRANSFAC

cathparse 

Generates DCF file from raw CATH files

domainnr 

Removes redundant domains from a DCF file

domainseqs 

Adds sequence records to a DCF file

domainsse 

Add secondary structure records to a DCF file

scopparse 

Generate DCF file from raw SCOP files

ssematch 

Search a DCF file for secondary structure matches

allversusall 

Sequence similarity data from all-versus-all comparison

seqnr 

Removes redundancy from DHF files

domainer 

Generates domain CCF files from protein CCF files

hetparse 

Converts heterogen group dictionary to EMBL-like format

pdbparse 

Parses PDB files and writes protein CCF files

pdbplus 

Add accessibility & secondary structure to a CCF file

pdbtosp 

Convert swissprot:PDB codes file to EMBL-like format

sites 

Generate residue-ligand CON files from CCF files

Database indexing

dbiblast 

Index a BLAST database

dbifasta 

Database indexing for fasta file databases

dbiflat 

Index a flat file database

dbigcg 

Index a GCG formatted database

dbxfasta 

Database b+tree indexing for fasta file databases

dbxflat 

Database b+tree indexing for flat file databases

dbxgcg 

Database b+tree indexing for GCG formatted databases

Utility tools

embossdata 

Finds or fetches data files read by EMBOSS programs

embossversion 

Writes the current EMBOSS version number

External / contributed packages

CBSTOOLS

The CBSTOOLS package is a set of wrappers to selected applications from the CBS group in Denmark.

CLUSTALOMEGA

A wrapper for the clustal omega application.

DOMAINATRIX

The DOMAINATRIX programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

DOMALIGN

The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

DOMSEARCH

The DOMSEARCH programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

EMBOSS

The latest stable version of EMBOSS (excluding bugfix patches from the 'fixes' directory hierarchy)

EMNU

The EMNU package is a simple EMBOSS menu system written by Gary Williams at HGMP.

ESIM4

The ESIM4 package is an EMBOSS conversion of the SIM4 package from Liliana Florea.

HMMER

A suite of application wrappers to the original hmmer v2.3.2 applications written by Sean Eddy. hmmer v2.3.2 must be installed on the same system as EMBOSS and the location of the hmmer executables must be defined in your path for EMBASSY HMMER to work.

IPRSCAN

The IPRSCAN package is a wrapper for the interproscan program.

MEME

The EMBASSY MEME package contains 'wrapper' applications providing an EMBOSS-style interface to the applications in the original MEME package version 4.0.0 developed by Timothy L. Bailey.

MIRA

The MIRA package is a fragment assembly program from Bastien Chevreux. The program was converted to EMBOSS by Alan Bleasby as two applications, one for EST assembly and one for shotgun fragment assembly

MSE

The MSE package is a multiple sequence editor. The program was contributed to the EMBOSS package by the author, Will Gilbert, as one of the first EMBASSY programs.

MYEMBOSS

A package for your own software developments.

MYEMBOSSDEMO

The MYEMBOSSDEMO package contains example applications using EMBOSS data types

PHYLIPNEW

The PHYLIPNEW programs are EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, version 3.69.

SIGNATURE

The SIGNATURE programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

STRUCTURE

The STRUCTURE programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

TOPO

The TOPO package is a graphics program to display membrane protein topology by Susan Jean Johns.

VIENNA

These programs are adapted from the VIENNA RNA package.