B.5. EMBASSY Applications (release R6)

Table B.4. EMBASSY Applications (available alongside EMBOSS release R6)
echloropReports presence of chloroplast transit peptides
elipopPrediction of lipoproteins
enetnglycReports N-glycosylation sites in human proteins
enetoglycReports mucin type GalNAc O-glycosylation sites in mammalian proteins
enetphosReports ser, thr and tyr phosphorylation sites in eukaryotic proteins
epropReports propeptide cleavage sites in proteins
esignalpReports protein signal cleavage sites
etmhmmReports transmembrane helices
eyinoyangReports O-(beta)-GlcNAc attachment sites
cathparseGenerates DCF file from raw CATH files
domainnrRemoves redundant domains from a DCF file
domainresoRemove low resolution domains from a DCF file
domainseqsAdds sequence records to a DCF file
domainsseAdd secondary structure records to a DCF file
scopparseGenerate DCF file from raw SCOP files
ssematchSearch a DCF file for secondary structure matches
allversusallSequence similarity data from all-versus-all comparison
domainalignGenerate alignments (DAF file) for nodes in a DCF file
domainrepReorder DCF file to identify representative structures
seqalignExtend alignments (DAF file) with sequences (DHF file)
seqfraggleRemoves fragment sequences from DHF files
seqnrRemoves redundancy from DHF files
seqsearchGenerate PSI-BLAST hits (DHF file) from a DAF file
seqsortRemove ambiguous classified sequences from DHF files
seqwordsGenerates DHF files from keyword search of UniProt
emnuSimple menu of EMBOSS applications
esim4Align an mRNA to a genomic DNA sequence
ehmmalignAlign sequences to an HMM profile
ehmmbuildBuild a profile HMM from an alignment
ehmmcalibrateCalibrate HMM search statistics
ehmmconvertConvert between profile HMM file formats
ehmmemitGenerate sequences from a profile HMM
ehmmfetchRetrieve an HMM from an HMM database
ehmmindexCreate a binary SSI index for an HMM database
ehmmpfamSearch one or more sequences against an HMM database
ehmmsearchSearch a sequence database with a profile HMM
eiprscanMotif detection
emastMotif detection
ememeMultiple EM for Motif Elicitation
ememetextMultiple EM for Motif Elicitation. Text file only
emiraMIRA fragment assembly program
emiraestMIRAest fragment assembly program
mseMultiple Sequence Editor
fcliqueLargest clique program
fconsenseMajority-rule and strict consensus tree
fcontmlGene frequency and continuous character Maximum Likelihood
fcontrastContinuous character Contrasts
fdiscbootBootstrapped discrete sites algorithm
fdnacompDNA compatibility algorithm
fdnadistNucleic acid sequence Distance Matrix program
fdnainvarNucleic acid sequence Invariants method
fdnamlEstimates nucleotide phylogeny by maximum likelihood
fdnamlkEstimates nucleotide phylogeny by maximum likelihood
fdnamoveInteractive DNA parsimony
fdnaparsDNA parsimony algorithm
fdnapennyPenny algorithm for DNA
fdollopDollo and polymorphism parsimony algorithm
fdolmoveInteractive Dollo or Polymorphism Parsimony
fdolpennyPenny algorithm Dollo or polymorphism
fdrawgramPlots a cladogram- or phenogram-like rooted tree diagram
fdrawtreePlots an unrooted tree diagram
ffactorMultistate to binary recoding program
ffitchFitch-Margoliash and Least-Squares Distance Methods
ffreqbootBootstrapped genetic frequencies algorithm
fgendistCompute genetic distances from gene frequencies
fkitschFitch-Margoliash method with contemporary tips
fmixMixed parsimony algorithm
fmoveInteractive mixed method parsimony
fneighborPhylogenies from distance matrix by N-J or UPGMA method
fparsDiscrete character parsimony
fpennyPenny algorithm, branch-and-bound
fpromlProtein phylogeny by maximum likelihood
fpromlkProtein phylogeny by maximum likelihood
fprotdistProtein distance algorithm
fprotparsProtein parsimony algorithm
frestbootBootstrapped restriction sites algorithm
frestdistDistance matrix from restriction sites or fragments
frestmlRestriction site maximum Likelihood method
fretreeInteractive tree rearrangement
fseqbootBootstrapped sequences algorithm
fseqbootallBootstrapped sequences algorithm
ftreedistDistances between trees
ftreedistpairDistances between two sets of trees
libgenGenerate discriminating elements from alignments
matgen3dGenerate a 3D-1D scoring matrix from CCF files
roconGenerates a hits file from comparing two DHF files
rocplotPerforms ROC analysis on hits files
siggenGenerates a sparse protein signature from an alignment
siggenligGenerates ligand-binding signatures from a CON file
sigscanGenerates hits (DHF file) from a signature search
sigscanligSearches ligand-signature library and writes hits (LHF file)
contactsGenerate intra-chain CON files from CCF files
domainerGenerates domain CCF files from protein CCF files
hetparseConverts heterogen group dictionary to EMBL-like format
interfaceGenerate inter-chain CON files from CCF files
pdbparseParses PDB files and writes protein CCF files
pdbplusAdd accessibility and secondary structure to a CCF file
pdbtospConvert swissprot:PDB codes file to EMBL-like format
sitesGenerate residue-ligand CON files from CCF files
topoDraws an image of a transmembrane protein
vrnaalifoldRNA alignment folding
vrnaalifoldpfRNA alignment folding with partition
vrnacofoldRNA cofolding
vrnacofoldconcRNA cofolding with concentrations
vrnacofoldpfRNA cofolding with partitioning
vrnadistanceRNA distances
vrnaduplexRNA duplex calculation
vrnaevalRNA eval
vrnaevalpairRNA eval with cofold
vrnafoldCalculate secondary structures of RNAs
vrnafoldpfSecondary structures of RNAs with partition
vrnaheatRNA melting
vrnainverseRNA sequences matching a structure
vrnalfoldCalculate locally stable secondary structures of RNAs
vrnaplotPlot vrnafold output
vrnasuboptCalculate RNA suboptimals