Crazybiocomputing.GitHub.io

List of EMBOSS applications

By Jean-Christophe Taveau.

A small utility page to easily search an application in the package. This page was calculated from release 6.6.

1- Applications of release 6.6

This list was created from the following genuine links...

• Applications sort by groups [L i n k]
• Applications sort alphabetically [L i n k]

2- List of applications with groups

• Acd — Acd file utilities
• 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 — Sequence comparison and alignment
• extractalign
• Extract regions from a sequence alignment
• Alignment consensus — Merging sequences to make a consensus
• 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 — Finding differences between sequences
• diffseq
• Compare and report features of two similar sequences
• Alignment dot plots — Dot plot sequence comparisons
• dotmatcher
• Draw a threshold dotplot of two sequences
• dotpath
• Draw a non-overlapping wordmatch dotplot of two sequences
• dottup
• Display a wordmatch dotplot of two sequences
• polydot
• Draw dotplots for all-against-all comparison of a sequence set
• Alignment global — Global sequence alignment
• est2genome
• Align EST sequences to genomic DNA sequence
• needle
• Needleman-Wunsch global alignment of two sequences
• needleall
• Many-to-many pairwise alignments of two sequence sets
• stretcher
• Needleman-Wunsch rapid global alignment of two sequences
• esim4
• Align an mRNA to a genomic DNA sequence
• Alignment local — Local sequence alignment
• 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
• Find regions of identity (exact matches) of two sequences
• 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)
• oalistat
• Statistics for multiple alignment files
• Alignment multiple —Multiple sequence alignment
• 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 alignment of nucleic coding regions from aligned proteins
• eomega
• Multiple sequence alignment (ClustalO wrapper)
• eomegapp
• Profile with profile (ClustalO wrapper)
• eomegash
• Sequence with HMM (ClustalO wrapper)
• eomegasp
• Sequence with profile (ClustalO wrapper)
• mse
• Multiple sequence editor
• Assembly fragment assembly — DNA sequence assembly
• emira
• MIRA fragment assembly program
• emiraest
• MIRAest fragment assembly program
• Data resources — Data resources
• cachedas
• Generate server cache file for DAS servers or for the DAS registry
• cachedbfetch
• Generate server cache file for Dbfetch/WSDbfetch data sources
• cacheebeyesearch
• Generate server cache file for EB-eye search domains
• cacheensembl
• Generate server cache file for an Ensembl server
• dbtell
• Display information about a public database
• servertell
• Display information about a public server
• showdb
• Display information on configured databases
• showserver
• Display information on configured servers
• Data retrieval — Data retrieval
• codcopy
• Copy and reformat a codon usage table
• seqret
• Read and write (return) sequences
• Data retrieval — Chemistry data retrieval
• infobase
• Return information on a given nucleotide base
• inforesidue
• Return information on a given amino acid residue
• Data retrieval — Sequence feature data retrieval
• featcopy
• Read and write a feature table
• featmerge
• Merge two overlapping feature tables
• Data retrieval — Ontology data retrieval
• edamdef
• Find EDAM ontology terms by definition
• edamhasinput
• Find EDAM ontology terms by has_input relation
• edamhasoutput
• Find EDAM ontology terms by has_output relation
• edamisformat
• Find EDAM ontology terms by is_format_of relation
• edamisid
• Find EDAM ontology terms by is_identifier_of relation
• edamname
• Find EDAM ontology terms by name
• godef
• Find GO ontology terms by definition
• goname
• Find GO ontology terms by name
• ontoget
• Get ontology term(s)
• ontogetcommon
• Get common ancestor for terms
• ontogetdown
• Get ontology term(s) by parent id
• ontogetobsolete
• Get ontology ontology terms
• ontogetroot
• Get ontology root terms by child identifier
• ontogetsibs
• Get ontology term(s) by id with common parent
• ontogetup
• Get ontology term(s) by id of child
• ontoisobsolete
• Report whether an ontology term id is obsolete
• ontotext
• Get ontology term(s) original full text
• Data retrieval — Resource data retrieval
• drfinddata
• Find public databases by data type
• drfindformat
• Find public databases by format
• drfindid
• Find public databases by identifier
• drfindresource
• Find public databases by resource
• drget
• Get data resource entries
• drtext
• Get data resource entries complete text
• Data retrieval — Sequence data retrieval
• abiview
• Display the trace in an ABI sequencer file
• coderet
• Extract CDS, mRNA and translations from feature tables
• entret
• Retrieve sequence entries from flatfile databases and files
• extractalign
• Extract regions from a sequence alignment
• infoalign
• Display basic information about a multiple sequence alignment
• infoseq
• Display basic information about sequences
• refseqget
• Get reference sequence
• seqxref
• Retrieve all database cross-references for a sequence entry
• seqxrefget
• Retrieve all cross-referenced data for a sequence entry
• showalign
• Display a multiple sequence alignment in pretty format
• variationget
• Get sequence variations
• whichdb
• Search all sequence databases for an entry and retrieve it
• Data retrieval — Sequence assembly data retrieval
• assemblyget
• Get assembly of sequence reads
• infoassembly
• Display information about assemblies
• Data retrieval — Text data retrieval
• drtext
• Get data resource entries complete text
• entret
• Retrieve sequence entries from flatfile databases and files
• ontotext
• Get ontology term(s) original full text
• textget
• Get text data entries
• textsearch
• Search the textual description of sequence(s)
• Data retrieval — Tool data retrieval
• 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
• Data retrieval — Url data retrieval
• urlget
• Get URLs of data resources
• Display — Publication-quality display
• abiview
• Display the trace in an ABI sequencer file
• cirdna
• Draw circular map of DNA constructs
• iep
• Calculate the isoelectric point of proteins
• lindna
• Draw linear maps of DNA constructs
• pepinfo
• Plot amino acid properties of a protein sequence in parallel
• pepnet
• Draw a helical net for a protein sequence
• pepwheel
• Draw a helical wheel diagram for a protein sequence
• plotorf
• Plot potential open reading frames in a nucleotide 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
• showfeat
• Display features of a sequence in pretty format
• showpep
• Display protein sequences with features in pretty format
• sixpack
• Display a DNA sequence with 6-frame translation and ORFs
• topo
• Draw an image of a transmembrane protein
• Documentation — Documentation
• seealso
• Find programs with similar function to a specified program
• tfm
• Display full documentation for an application
• wossdata
• Find programs by EDAM data
• wossinput
• Find programs by EDAM input data
• wossname
• Find programs by keywords in their short description
• wossoperation
• Find programs by EDAM operation
• wossoutput
• Find programs by EDAM output data
• wossparam
• Find programs by EDAM parameter
• wosstopic
• Find programs by EDAM topic
• Edit — Data file and content editing
• aligncopy
• Read and write alignments
• aligncopypair
• Read and write pairs from alignments
• biosed
• Replace or delete sequence sections
• codcopy
• Copy and reformat a codon usage table
• cutseq
• Remove a section from a sequence
• degapseq
• Remove non-alphabetic (e.g. gap) characters from sequences
• descseq
• Alter the name or description of a sequence
• entret
• Retrieve 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
• Read and write a feature table
• featmerge
• Merge two overlapping feature tables
• featreport
• Read and write a feature table
• feattext
• Return a feature table original text
• 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
• Mask all ambiguity characters in nucleotide sequences with N
• maskambigprot
• Mask 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 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
• nthseqset
• Read and write (return) one set of sequences from many
• pasteseq
• Insert one sequence into another
• revseq
• Reverse and complement a nucleotide sequence
• seqcount
• Read and count sequences
• seqret
• Read and write (return) sequences
• seqretsetall
• Read and write (return) many sets of sequences
• seqretsplit
• Read sequences and write them to individual files
• sizeseq
• Sort sequences by size
• skipredundant
• Remove redundant sequences from an input set
• skipseq
• Read and write (return) sequences, skipping first few
• splitsource
• Split sequence(s) into original source sequences
• 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)
• trimspace
• Remove extra whitespace from an ASCII text file
• union
• Concatenate multiple sequences into a single sequence
• vectorstrip
• Remove vectors from the ends of nucleotide sequence(s)
• yank
• Add a sequence reference (a full USA) to a list file
• seqfraggle
• Remove fragment sequences from DHF files
• Enzyme kinetics — Enzyme kinetics calculations
• findkm
• Calculate and plot enzyme reaction data
• Feature tables — Manipulation and display of sequence annotation
• extractfeat
• Extract features from sequence(s)
• maskfeat
• Write a sequence with masked features
• showfeat
• Display features of a sequence in pretty format
• twofeat
• Find neighbouring pairs of features in sequence(s)
• HMM — Hidden markov model analysis
• 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
• libgen
• Generate discriminating elements from alignments
• Menus — Menu interface(s)
• emnu
• Simple menu of EMBOSS applications
• Nucleic — Nucleic acid secondary structure
• banana
• Plot bending and curvature data for B-DNA
• btwisted
• Calculate the twisting in a B-DNA sequence
• einverted
• Find inverted repeats in nucleotide sequences
• sirna
• Find siRNA duplexes in mRNA
• ovrnaalifold
• Calculate secondary structures for a set of aligned RNAs
• ovrnaalifoldpf
• Calculate secondary structures for a set of aligned RNAs (partition)
• ovrnacofold
• Calculate secondary structures of RNA dimers
• ovrnacofoldconc
• Calculate secondary structures of RNA dimers (concentrations)
• ovrnacofoldpf
• Calculate secondary structures of RNA dimers (partitioning)
• ovrnadistance
• Calculate distances between RNA secondary structures
• ovrnaduplex
• Predict RNA duplex (hybridization) sites and structure
• ovrnaeval
• Calculate energy of RNA sequences with a given secondary structure
• ovrnaevalpair
• Calculate energy of RNA sequences on given secondary structure
• ovrnafold
• Calculate min. energy RNA structure / pair probabilities (partition)
• ovrnafoldpf
• Calculate min. energy RNA structure / pair probabilities
• ovrnaheat
• Calculate specific heat of RNA melting
• ovrnainverse
• Find RNA sequences with a given secondary structure
• ovrnalfold
• Calculate locally stable secondary structures of RNAs
• ovrnaplot
• Draw RNA secondary structures
• ovrnasubopt
• Calculate suboptimal secondary structure of RNA
• vrna2dfold
• Calculate RNA structures and samples of k,l neighbourhoods
• vrnaaliduplex
• RNA duplex calculation for two sequence alignments
• vrnaalifold
• Calculate secondary structures for a set of aligned RNAs
• vrnaalifoldpf
• Calculate secondary structures for a set of aligned RNAs (partition)
• vrnacofold
• Calculate secondary structures of RNA dimers
• vrnacofoldconc
• Calculate secondary structures of RNA dimers (concentrations)
• vrnacofoldpf
• Calculate secondary structures of RNA dimers (partitioning)
• vrnadistance
• Calculate distances between RNA secondary structures
• vrnaduplex
• Predict RNA duplex (hybridization) sites and structure
• vrnaeval
• Calculate energy of RNA sequences with a given secondary structure
• vrnaevalpair
• Calculate energy of RNA sequences on given secondary structure
• vrnafold
• Calculate min. energy RNA secondary structures and pair probabilities
• vrnafoldpf
• Calculate min. energy RNA structures / pair probabilities (partition)
• vrnaheat
• Calculate specific heat of RNA melting
• vrnainverse
• Find RNA sequences with a given secondary structure
• vrnalalifoldpf
• Calculate secondary structures for a set of aligned RNAs (partition)
• vrnalfold
• Calculate locally stable secondary structures of RNAs
• vrnalfoldz
• Calculate locally stable secondary structures of RNAs plus zscore
• vrnapkplex
• Calculate RNA structures plus pseudoknots
• vrnaplfold
• Compute avg. pair probabilities for local base pairs in RNA sequences
• vrnaplot
• Draw RNA secondary structures
• vrnasubopt
• Calculate suboptimal secondary structures of RNAs
• Nucleic — Codon usage analysis
• cai
• Calculate codon adaptation index
• chips
• Calculate Nc codon usage statistic
• codcmp
• Codon usage table comparison
• codcopy
• Copy and reformat a codon usage table
• cusp
• Create a codon usage table from nucleotide sequence(s)
• syco
• Draw synonymous codon usage statistic plot for a nucleotide sequence
• Nucleic — Composition of nucleotide sequences
• 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
• Calculate nucleic acid melting temperature
• density
• Draw a nucleic acid density plot
• freak
• Generate residue/base frequency table or plot
• isochore
• Plot isochores in DNA sequences
• wordcount
• Count and extract unique words in molecular sequence(s)
• Nucleic — CpG island detection and analysis
• 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 — Nucleic acid functional sites
• marscan
• Find matrix/scaffold recognition (MRS) signatures in DNA sequences
• sirna
• Find siRNA duplexes in mRNA
• trimest
• Remove poly-A tails from nucleotide sequences
• Nucleic — Predictions of genes and other genomic features
• checktrans
• Report STOP codons and ORF statistics of a protein
• getorf
• Find and extract open reading frames (ORFs)
• marscan
• Find 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 statistic 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 — Nucleic acid motif searches
• dreg
• Regular expression search of nucleotide sequence(s)
• fuzznuc
• Search for patterns in nucleotide sequences
• fuzztran
• Search for patterns in protein sequences (translated)
• Nucleic — Nucleic acid sequence mutation
• msbar
• Mutate a sequence
• shuffleseq
• Shuffle a set of sequences maintaining composition
• Nucleic — Primer prediction
• eprimer3
• Pick PCR primers and hybridization oligos
• eprimer32
• Pick 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 — Nucleic acid profile generation and searching
• 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 — Nucleic acid physicochemical properties
• banana
• Plot bending and curvature data for B-DNA
• btwisted
• Calculate the twisting in a B-DNA sequence
• dan
• Calculate nucleic acid melting temperature
• vrnaheat
• Calculate specific heat of RNA melting
• Nucleic — Nucleic acid repeat detection
• einverted
• Find inverted repeats in nucleotide sequences
• equicktandem
• Find tandem repeats in nucleotide sequences
• etandem
• Find tandem repeats in a nucleotide sequence
• palindrome
• Find inverted repeats in nucleotide sequence(s)
• Nucleic — Restriction enzyme sites in nucleotide sequences
• 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
• Display sequences with features in pretty format
• silent
• Find restriction sites to insert (mutate) with no translation change
• Nucleic RNA folding — RNA folding methods and analysis
• ovrnaalifold
• Calculate secondary structures for a set of aligned RNAs
• ovrnaalifoldpf
• Calculate secondary structures for a set of aligned RNAs (partition)
• ovrnacofold
• Calculate secondary structures of RNA dimers
• ovrnacofoldconc
• Calculate secondary structures of RNA dimers (concentrations)
• ovrnacofoldpf
• Calculate secondary structures of RNA dimers (partitioning)
• ovrnadistance
• Calculate distances between RNA secondary structures
• ovrnaduplex
• Predict RNA duplex (hybridization) sites and structure
• ovrnaeval
• Calculate energy of RNA sequences with a given secondary structure
• ovrnaevalpair
• Calculate energy of RNA sequences on given secondary structure
• ovrnafold
• Calculate min. energy RNA structure / pair probabilities (partition)
• ovrnafoldpf
• Calculate min. energy RNA structure / pair probabilities
• ovrnaheat
• Calculate specific heat of RNA melting
• ovrnainverse
• Find RNA sequences with a given secondary structure
• ovrnalfold
• Calculate locally stable secondary structures of RNAs
• ovrnaplot
• Draw RNA secondary structures
• ovrnasubopt
• Calculate suboptimal secondary structure of RNA
• vrna2dfold
• Calculate RNA structures and samples of k,l neighbourhoods
• vrnaaliduplex
• RNA duplex calculation for two sequence alignments
• vrnaalifold
• Calculate secondary structures for a set of aligned RNAs
• vrnaalifoldpf
• Calculate secondary structures for a set of aligned RNAs (partition)
• vrnacofold
• Calculate secondary structures of RNA dimers
• vrnacofoldconc
• Calculate secondary structures of RNA dimers (concentrations)
• vrnacofoldpf
• Calculate secondary structures of RNA dimers (partitioning)
• vrnadistance
• Calculate distances between RNA secondary structures
• vrnaduplex
• Predict RNA duplex (hybridization) sites and structure
• vrnaeval
• Calculate energy of RNA sequences with a given secondary structure
• vrnaevalpair
• Calculate energy of RNA sequences on given secondary structure
• vrnafold
• Calculate min. energy RNA secondary structures and pair probabilities
• vrnafoldpf
• Calculate min. energy RNA structures / pair probabilities (partition)
• vrnaheat
• Calculate specific heat of RNA melting
• vrnainverse
• Find RNA sequences with a given secondary structure
• vrnalalifoldpf
• Calculate secondary structures for a set of aligned RNAs (partition)
• vrnalfold
• Calculate locally stable secondary structures of RNAs
• vrnalfoldz
• Calculate locally stable secondary structures of RNAs plus zscore
• vrnapkplex
• Calculate RNA structures plus pseudoknots
• vrnaplfold
• Compute avg. pair probabilities for local base pairs in RNA sequences
• vrnaplot
• Draw RNA secondary structures
• vrnasubopt
• Calculate suboptimal secondary structures of RNAs
• Nucleic transcription —Transcription factors, promoters and terminator prediction
• jaspscan
• Scan DNA sequences for transcription factors
• marscan
• Find matrix/scaffold recognition (MRS) signatures in DNA sequences
• tfscan
• Identify transcription factor binding sites in DNA sequences
• Nucleic translation —Translation of nucleotide sequence to protein sequence
• backtranambig
• Back-translate a protein sequence to ambiguous nucleotide sequence
• backtranseq
• Back-translate a protein sequence to a nucleotide sequence
• checktrans
• Report STOP codons and ORF statistics of a protein
• 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
• Display sequences with features in pretty format
• sixpack
• Display a DNA sequence with 6-frame translation and ORFs
• transeq
• Translate nucleic acid sequences
• Ontology — Ontologies
• ontocount
• Count ontology term(s)
• ontoget
• Get ontology term(s)
• ontogetcommon
• Get common ancestor for terms
• ontogetdown
• Get ontology term(s) by parent id
• ontogetobsolete
• Get ontology ontology terms
• ontogetroot
• Get ontology root terms by child identifier
• ontogetsibs
• Get ontology term(s) by id with common parent
• ontogetup
• Get ontology term(s) by id of child
• ontoisobsolete
• Report whether an ontology term id is obsolete
• ontotext
• Get ontology term(s) original full text
• Ontology edam — Edam ontology
• drfinddata
• Find public databases by data type
• drfindformat
• Find public databases by format
• drfindid
• Find public databases by identifier
• drfindresource
• Find public databases by resource
• edamdef
• Find EDAM ontology terms by definition
• edamhasinput
• Find EDAM ontology terms by has_input relation
• edamhasoutput
• Find EDAM ontology terms by has_output relation
• edamisformat
• Find EDAM ontology terms by is_format_of relation
• edamisid
• Find EDAM ontology terms by is_identifier_of relation
• edamname
• Find EDAM ontology terms by name
• wossdata
• Find programs by EDAM data
• wossinput
• Find programs by EDAM input data
• wossoperation
• Find programs by EDAM operation
• wossoutput
• Find programs by EDAM output data
• wossparam
• Find programs by EDAM parameter
• wosstopic
• Find programs by EDAM topic
• Ontology go — Go gene ontology
• godef
• Find GO ontology terms by definition
• goname
• Find GO ontology terms by name
• Ontology taxonomy — Ncbi taxonomy
• taxget
• Get taxon(s)
• taxgetdown
• Get descendants of taxon(s)
• taxgetrank
• Get parents of taxon(s)
• taxgetspecies
• Get all species under taxon(s)
• taxgetup
• Get parents of taxon(s)
• Phylogeny consensus — Phylogenetic consensus methods
• econsense
• Majority-rule and strict consensus tree
• fconsense
• Majority-rule and strict consensus tree
• ftreedist
• Calculate distances between trees
• ftreedistpair
• Calculate distance between two sets of trees
• Phylogeny — Phylogenetic continuous character methods
• econtml
• Continuous character maximum likelihood method
• econtrast
• Continuous character contrasts
• fcontrast
• Continuous character contrasts
• Phylogeny — 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
• Phylogeny — 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
• Phylogeny — Phylogenetic gene frequency methods
• egendist
• Genetic distance matrix program
• fcontml
• Gene frequency and continuous character maximum likelihood
• fgendist
• Compute genetic distances from gene frequencies
• Phylogeny — Phylogenetic molecular sequence methods
• distmat
• Create a distance matrix from a multiple sequence alignment
• 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
• Estimate 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
• Calculate distance matrix from restriction sites or fragments
• frestml
• Restriction site maximum likelihood method
• fseqboot
• Bootstrapped sequences algorithm
• fseqbootall
• Bootstrapped sequences algorithm
• Phylogeny — Phylogenetic tree drawing methods
• fdrawgram
• Plots a cladogram- or phenogram-like rooted tree diagram
• fdrawtree
• Plots an unrooted tree diagram
• fretree
• Interactive tree rearrangement
• Protein 2d structure — Protein secondary structure
• garnier
• Predict protein secondary structure using GOR method
• helixturnhelix
• Identify nucleic acid-binding motifs in protein sequences
• pepcoil
• Predict 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
• Protein 3d structure — Protein tertiary structure
• psiphi
• Calculates phi and psi torsion angles from protein coordinates
• domainreso
• Remove low resolution domains from a DCF file
• domainrep
• Reorder DCF file to identify representative structures
• contacts
• Generate intra-chain CON files from CCF files
• interface
• Generate inter-chain CON files from CCF files
• Protein composition — Composition of protein sequences
• backtranambig
• Back-translate a protein sequence to ambiguous nucleotide sequence
• backtranseq
• Back-translate a protein sequence to a nucleotide sequence
• 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
• mwcontam
• Find weights common to multiple molecular weights files
• mwfilter
• Filter noisy data from molecular weights file
• oddcomp
• Identify proteins with specified sequence word composition
• pepdigest
• Report on protein proteolytic enzyme or reagent cleavage sites
• pepinfo
• Plot amino acid properties of a protein sequence in parallel
• pepstats
• Calculate statistics of protein properties
• wordcount
• Count and extract unique words in molecular sequence(s)
• Protein domains — Protein domain analysis
• helixturnhelix
• Identify nucleic acid-binding motifs in protein sequences
• pepcoil
• Predict coiled coil regions in protein sequences
• cathparse
• Generate DCF file from raw CATH files
• domainnr
• Remove redundant domains from a DCF file
• domainseqs
• Add 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
• 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
• Remove fragment sequences from DHF files
• seqsort
• Remove ambiguous classified sequences from DHF files
• seqwords
• Generate DHF files from keyword search of UniProt
• libgen
• Generate discriminating elements from alignments
• matgen3d
• Generate a 3D-1D scoring matrix from CCF files
• rocon
• Generate a hits file from comparing two DHF files
• rocplot
• Perform ROC analysis on hits files
• Protein functional sites — Protein functional sites
• sigcleave
• Report on signal cleavage sites in a protein sequence
• tmap
• Predict and plot transmembrane segments in protein sequences
• echlorop
• Report presence of chloroplast transit peptides
• elipop
• Predict lipoproteins
• esignalp
• Report protein signal cleavage sites
• etmhmm
• Reports transmembrane helices
• siggenlig
• Generate ligand-binding signatures from a CON file
• sigscan
• Generate hits (DHF file) from a signature search
• topo
• Draw an image of a transmembrane protein
• Protein modifications — Protein post-translational modifications
• enetnglyc
• Report N-glycosylation sites in human proteins
• enetoglyc
• Reports mucin type GalNAc O-glycosylation sites in mammalian proteins
• enetphos
• Report Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins
• eprop
• Report propeptide cleavage sites in proteins
• esignalp
• Report protein signal cleavage sites
• eyinoyang
• Report O-(beta)-GlcNAc attachment sites
• Protein motifs — Protein motif searches
• antigenic
• Find antigenic sites in proteins
• epestfind
• Find PEST motifs as potential proteolytic cleavage sites
• fuzzpro
• Search for patterns in protein sequences
• fuzztran
• Search for patterns in protein sequences (translated)
• patmatdb
• Search protein sequences with a sequence motif
• patmatmotifs
• Scan a protein sequence with motifs from the PROSITE database
• preg
• Regular expression search of protein sequence(s)
• pscan
• Scan protein sequence(s) with fingerprints from the PRINTS database
• sigcleave
• Report on signal cleavage sites in a protein sequence
• elipop
• Predict lipoproteins
• eiprscan
• Motif detection
• omeme
• Motif detection
• emast
• Motif detection
• ememe
• Multiple EM for motif elicitation
• ememetext
• Multiple EM for motif elicitation, text file only
• Protein mutation — Protein sequence mutation
• msbar
• Mutate a sequence
• shuffleseq
• Shuffle a set of sequences maintaining composition
• Protein profiles — Protein profile generation and searching
• 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
• seqsearch
• Generate PSI-BLAST hits (DHF file) from a DAF file
• siggen
• Generate 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 and writes hits (LHF file)
• Protein properties — Protein physicochemical properties
• charge
• Draw a protein charge plot
• hmoment
• Calculate and plot hydrophobic moment for protein sequence(s)
• iep
• Calculate the isoelectric point of proteins
• octanol
• Draw a White-Wimley protein hydropathy plot
• pepinfo
• Plot amino acid properties of a protein sequence in parallel
• pepstats
• Calculate statistics of protein properties
• pepwindow
• Draw a hydropathy plot for a protein sequence
• pepwindowall
• Draw Kyte-Doolittle hydropathy plot for a protein alignment
• Test — Testing tools, not for general use.
• crystalball
• Answer every drug discovery question about a sequence
• Utils — Utility tools
• embossdata
• Find and retrieve EMBOSS data files
• embossupdate
• Checks for more recent updates to EMBOSS
• embossversion
• Report the current EMBOSS version number
• Utils database creation — Database installation
• aaindexextract
• Extract amino acid property data from AAINDEX
• cutgextract
• Extract codon usage tables from CUTG database
• jaspextract
• Extract data from JASPAR
• printsextract
• Extract data from PRINTS database for use by pscan
• prosextract
• Process 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
• cathparse
• Generate DCF file from raw CATH files
• domainnr
• Remove redundant domains from a DCF file
• domainseqs
• Add 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
• Remove redundancy from DHF files
• domainer
• Generate domain CCF files from protein CCF files
• hetparse
• Convert heterogen group dictionary to EMBL-like format
• pdbparse
• Parse PDB files and writes protein CCF files
• pdbplus
• Add accessibility and 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
• Utils database indexing — Database indexing
• dbiblast
• Index a BLAST database
• dbifasta
• Index a fasta file database
• dbiflat
• Index a flat file database
• dbigcg
• Index a GCG formatted database
• dbxcompress
• Compress an uncompressed dbx index
• dbxedam
• Index the EDAM ontology using b+tree indices
• 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
• dbxobo
• Index an obo ontology using b+tree indices
• dbxreport
• Validate index and report internals for dbx databases
• dbxresource
• Index a data resource catalogue using b+tree indices
• dbxstat
• Dump statistics for dbx databases
• dbxtax
• Index NCBI taxonomy using b+tree indices
• dbxuncompress
• Uncompress a compressed dbx index