B.6. All Applications (by group)

B.6.1. Applications in group Acd

Table B.5. Applications in group Acd
ApplicationDescription
acdcTest an application ACD file
acdprettyCorrectly reformat an application ACD file
acdtableGenerate an HTML table of parameters from an application ACD file
acdtraceTrace processing of an application ACD file (for testing)
acdvalidValidate an application ACD file

B.6.2. Applications in group Alignment:consensus

Table B.6. Applications in group Alignment:consensus
ApplicationDescription
consCreate a consensus sequence from a multiple alignment
consambigCreate an ambiguous consensus sequence from a multiple alignment
megamergerMerge two large overlapping DNA sequences
mergerMerge two overlapping sequences

B.6.3. Applications in group Alignment:differences

Table B.7. Applications in group Alignment:differences
ApplicationDescription
diffseqCompare and report features of two similar sequences

B.6.4. Applications in group Alignment:dot plots

Table B.8. Applications in group Alignment:dot plots
ApplicationDescription
dotmatcherDraw a threshold dotplot of two sequences
dotpathDraw a non-overlapping wordmatch dotplot of two sequences
dottupDisplays a wordmatch dotplot of two sequences
polydotDraw dotplots for all-against-all comparison of a sequence set

B.6.5. Applications in group Alignment:global

Table B.9. Applications in group Alignment:global
ApplicationDescription
est2genomeAlign EST sequences to genomic DNA sequence
needleNeedleman-Wunsch global alignment of two sequences
needleallMany-to-many pairwise alignments of two sequence sets
stretcherNeedleman-Wunsch rapid global alignment of two sequences

B.6.6. Applications in group Alignment:local

Table B.10. Applications in group Alignment:local
ApplicationDescription
matcherWaterman-Eggert local alignment of two sequences
seqmatchallAll-against-all word comparison of a sequence set
supermatcherCalculate approximate local pair-wise alignments of larger sequences
waterSmith-Waterman local alignment of sequences
wordfinderMatch large sequences against one or more other sequences
wordmatchFinds regions of identity (exact matches) of two sequences

B.6.7. Applications in group Alignment:multiple

Table B.11. Applications in group Alignment:multiple
ApplicationDescription
edialignLocal multiple alignment of sequences
emmaMultiple sequence alignment (ClustalW wrapper)
infoalignDisplay basic information about a multiple sequence alignment
plotconPlot conservation of a sequence alignment
prettyplotDraw a sequence alignment with pretty formatting
showalignDisplay a multiple sequence alignment in pretty format
tranalignGenerate an alignment of nucleic coding regions from aligned proteins

B.6.8. Applications in group Display

Table B.12. Applications in group Display
ApplicationDescription
abiviewDisplay the trace in an ABI sequencer file
cirdnaDraws circular maps of DNA constructs
lindnaDraws linear maps of DNA constructs
pepnetDraw a helical net for a protein sequence
pepwheelDraw a helical wheel diagram for a protein sequence
prettyplotDraw a sequence alignment with pretty formatting
prettyseqWrite a nucleotide sequence and its translation to file
remapDisplay restriction enzyme binding sites in a nucleotide sequence
seealsoFinds programs with similar function to a specified program
showalignDisplay a multiple sequence alignment in pretty format
showdbDisplays information on configured databases
showfeatDisplay features of a sequence in pretty format
showpepDisplays protein sequences with features in pretty format
showseqDisplays sequences with features in pretty format
sixpackDisplay a DNA sequence with 6-frame translation and ORFs
textsearchSearch the textual description of sequence(s)

B.6.9. Applications in group Edit

Table B.13. Applications in group Edit
ApplicationDescription
aligncopyReads and writes alignments
aligncopypairReads and writes pairs from alignments
biosedReplace or delete sequence sections
codcopyCopy and reformat a codon usage table
cutseqRemoves a section from a sequence
degapseqRemoves non-alphabetic (e.g. gap) characters from sequences
descseqAlter the name or description of a sequence
entretRetrieves sequence entries from flatfile databases and files
extractalignExtract regions from a sequence alignment
extractfeatExtract features from sequence(s)
extractseqExtract regions from a sequence
featcopyReads and writes a feature table
featreportReads and writes a feature table
listorWrite a list file of the logical OR of two sets of sequences
makenucseqCreate random nucleotide sequences
makeprotseqCreate random protein sequences
maskambignucMasks all ambiguity characters in nucleotide sequences with N
maskambigprotMasks all ambiguity characters in protein sequences with X
maskfeatWrite a sequence with masked features
maskseqWrite a sequence with masked regions
newseqCreate a sequence file from a typed-in sequence
nohtmlRemove mark-up (e.g. HTML tags) from an ASCII text file
noreturnRemove carriage return from ASCII files
nospaceRemove all whitespace from an ASCII text file
notabReplace tabs with spaces in an ASCII text file
notseqWrite to file a subset of an input stream of sequences
nthseqWrite to file a single sequence from an input stream of sequences
nthseqsetReads and writes (returns) one set of sequences from many
pasteseqInsert one sequence into another
revseqReverse and complement a nucleotide sequence
seqretReads and writes (returns) sequences
seqretsetallReads and writes (returns) many sets of sequences
seqretsplitReads sequences and writes them to individual files
sizeseqSort sequences by size
skipredundantRemove redundant sequences from an input set
skipseqReads and writes (returns) sequences, skipping first few
splitsourceSplit sequence(s) into original source sequences
splitterSplit sequence(s) into smaller sequences
trimestRemove poly-A tails from nucleotide sequences
trimseqRemove unwanted characters from start and end of sequence(s)
trimspaceRemove extra whitespace from an ASCII text file
unionConcatenate multiple sequences into a single sequence
vectorstripRemoves vectors from the ends of nucleotide sequence(s)
yankAdd a sequence reference (a full USA) to a list file

B.6.10. Applications in group Enzyme kinetics

Table B.14. Applications in group Enzyme kinetics
ApplicationDescription
findkmCalculate and plot enzyme reaction data

B.6.11. Applications in group Feature tables

Table B.15. Applications in group Feature tables
ApplicationDescription
coderetExtract CDS, mRNA and translations from feature tables
extractfeatExtract features from sequence(s)
maskfeatWrite a sequence with masked features
showfeatDisplay features of a sequence in pretty format
twofeatFinds neighbouring pairs of features in sequence(s)

B.6.12. Applications in group Information

Table B.16. Applications in group Information
ApplicationDescription
infoalignDisplay basic information about a multiple sequence alignment
infobaseReturn information on a given nucleotide base
inforesidueReturn information on a given amino acid residue
infoseqDisplay basic information about sequences
seealsoFinds programs with similar function to a specified program
showdbDisplays information on configured databases
textsearchSearch the textual description of sequence(s)
tfmDisplays full documentation for an application
whichdbSearch all sequence databases for an entry and retrieve it
wossnameFinds programs by keywords in their short description

B.6.13. Applications in group Nucleic:2d structure

Table B.17. Applications in group Nucleic:2d structure
ApplicationDescription
einvertedFinds inverted repeats in nucleotide sequences

B.6.14. Applications in group Nucleic:codon usage

Table B.18. Applications in group Nucleic:codon usage
ApplicationDescription
caiCalculate codon adaptation index
chipsCalculates Nc codon usage statistic
codcmpCodon usage table comparison
cuspCreate a codon usage table from nucleotide sequence(s)
sycoDraw synonymous codon usage statistic plot for a nucleotide sequence

B.6.15. Applications in group Nucleic:composition

Table B.19. Applications in group Nucleic:composition
ApplicationDescription
bananaPlot bending and curvature data for B-DNA
btwistedCalculate the twisting in a B-DNA sequence
chaosDraw a chaos game representation plot for a nucleotide sequence
compseqCalculate the composition of unique words in sequences
danCalculates nucleic acid melting temperature
densityDraw a nucleic acid density plot
freakGenerate residue/base frequency table or plot
isochorePlots isochores in DNA sequences
sirnaFinds siRNA duplexes in mRNA
wordcountCount and extract unique words in molecular sequence(s)

B.6.16. Applications in group Nucleic:cpg islands

Table B.20. Applications in group Nucleic:cpg islands
ApplicationDescription
cpgplotIdentify and plot CpG islands in nucleotide sequence(s)
cpgreportIdentify and report CpG-rich regions in nucleotide sequence(s)
geeceeCalculate fractional GC content of nucleic acid sequences
newcpgreportIdentify CpG islands in nucleotide sequence(s)
newcpgseekIdentify and report CpG-rich regions in nucleotide sequence(s)

B.6.17. Applications in group Nucleic:gene finding

Table B.21. Applications in group Nucleic:gene finding
ApplicationDescription
getorfFinds and extracts open reading frames (ORFs)
marscanFinds matrix/scaffold recognition (MRS) signatures in DNA sequences
plotorfPlot potential open reading frames in a nucleotide sequence
showorfDisplay a nucleotide sequence and translation in pretty format
sixpackDisplay a DNA sequence with 6-frame translation and ORFs
sycoDraw synonymous codon usage statistic plot for a nucleotide sequence
tcodeIdentify protein-coding regions using Fickett TESTCODE statistic
wobblePlot third base position variability in a nucleotide sequence

B.6.18. Applications in group Nucleic:motifs

Table B.22. Applications in group Nucleic:motifs
ApplicationDescription
dregRegular expression search of nucleotide sequence(s)
fuzznucSearch for patterns in nucleotide sequences
fuzztranSearch for patterns in protein sequences (translated)
marscanFinds matrix/scaffold recognition (MRS) signatures in DNA sequences

B.6.19. Applications in group Nucleic:mutation

Table B.23. Applications in group Nucleic:mutation
ApplicationDescription
msbarMutate a sequence
shuffleseqShuffles a set of sequences maintaining composition

B.6.20. Applications in group Nucleic:primers

Table B.24. Applications in group Nucleic:primers
ApplicationDescription
eprimer3Picks PCR primers and hybridization oligos
primersearchSearch DNA sequences for matches with primer pairs
stssearchSearch a DNA database for matches with a set of STS primers

B.6.21. Applications in group Nucleic:profiles

Table B.25. Applications in group Nucleic:profiles
ApplicationDescription
profitScan one or more sequences with a simple frequency matrix
prophecyCreate frequency matrix or profile from a multiple alignment
prophetScan one or more sequences with a Gribskov or Henikoff profile

B.6.22. Applications in group Nucleic:repeats

Table B.26. Applications in group Nucleic:repeats
ApplicationDescription
einvertedFinds inverted repeats in nucleotide sequences
equicktandemFinds tandem repeats in nucleotide sequences
etandemFinds tandem repeats in a nucleotide sequence
palindromeFinds inverted repeats in nucleotide sequence(s)

B.6.23. Applications in group Nucleic:restriction

Table B.27. Applications in group Nucleic:restriction
ApplicationDescription
recoderFind restriction sites to remove (mutate) with no translation change
redataRetrieve information from REBASE restriction enzyme database
remapDisplay restriction enzyme binding sites in a nucleotide sequence
restoverFind restriction enzymes producing a specific overhang
restrictReport restriction enzyme cleavage sites in a nucleotide sequence
showseqDisplays sequences with features in pretty format
silentFind restriction sites to insert (mutate) with no translation change

B.6.24. Applications in group Nucleic:transcription

Table B.28. Applications in group Nucleic:transcription
ApplicationDescription
jaspscanScans DNA sequences for transcription factors
tfscanIdentify transcription factor binding sites in DNA sequences

B.6.25. Applications in group Nucleic:translation

Table B.29. Applications in group Nucleic:translation
ApplicationDescription
backtranambigBack-translate a protein sequence to ambiguous nucleotide sequence
backtranseqBack-translate a protein sequence to a nucleotide sequence
coderetExtract CDS, mRNA and translations from feature tables
plotorfPlot potential open reading frames in a nucleotide sequence
prettyseqWrite a nucleotide sequence and its translation to file
remapDisplay restriction enzyme binding sites in a nucleotide sequence
showorfDisplay a nucleotide sequence and translation in pretty format
showseqDisplays sequences with features in pretty format
sixpackDisplay a DNA sequence with 6-frame translation and ORFs
transeqTranslate nucleic acid sequences

B.6.26. Applications in group Phylogeny:molecular sequence

Table B.30. Applications in group Phylogeny:molecular sequence
ApplicationDescription
distmatCreate a distance matrix from a multiple sequence alignment

B.6.27. Applications in group Protein:2d structure

Table B.31. Applications in group Protein:2d structure
ApplicationDescription
garnierPredicts protein secondary structure using GOR method
helixturnhelixIdentify nucleic acid-binding motifs in protein sequences
hmomentCalculate and plot hydrophobic moment for protein sequence(s)
pepcoilPredicts coiled coil regions in protein sequences
pepnetDraw a helical net for a protein sequence
pepwheelDraw a helical wheel diagram for a protein sequence
tmapPredict and plot transmembrane segments in protein sequences

B.6.28. Applications in group Protein:3d structure

Table B.32. Applications in group Protein:3d structure
ApplicationDescription
psiphiCalculates phi and psi torsion angles from protein coordinates

B.6.29. Applications in group Protein:composition

Table B.33. Applications in group Protein:composition
ApplicationDescription
backtranambigBack-translate a protein sequence to ambiguous nucleotide sequence
backtranseqBack-translate a protein sequence to a nucleotide sequence
chargeDraw a protein charge plot
checktransReports STOP codons and ORF statistics of a protein
compseqCalculate the composition of unique words in sequences
emowseSearch protein sequences by digest fragment molecular weight
freakGenerate residue/base frequency table or plot
iepCalculate the isoelectric point of proteins
mwcontamFind weights common to multiple molecular weights files
mwfilterFilter noisy data from molecular weights file
octanolDraw a White-Wimley protein hydropathy plot
pepinfoPlot amino acid properties of a protein sequence in parallel
pepstatsCalculates statistics of protein properties
pepwindowDraw a hydropathy plot for a protein sequence
pepwindowallDraw Kyte-Doolittle hydropathy plot for a protein alignment
wordcountCount and extract unique words in molecular sequence(s)

B.6.30. Applications in group Protein:motifs

Table B.34. Applications in group Protein:motifs
ApplicationDescription
antigenicFinds antigenic sites in proteins
digestReports on protein proteolytic enzyme or reagent cleavage sites
epestfindFinds PEST motifs as potential proteolytic cleavage sites
fuzzproSearch for patterns in protein sequences
fuzztranSearch for patterns in protein sequences (translated)
helixturnhelixIdentify nucleic acid-binding motifs in protein sequences
oddcompIdentify proteins with specified sequence word composition
patmatdbSearches protein sequences with a sequence motif
patmatmotifsScan a protein sequence with motifs from the PROSITE database
pepcoilPredicts coiled coil regions in protein sequences
pregRegular expression search of protein sequence(s)
pscanScans protein sequence(s) with fingerprints from the PRINTS database
sigcleaveReports on signal cleavage sites in a protein sequence

B.6.31. Applications in group Protein:mutation

Table B.35. Applications in group Protein:mutation
ApplicationDescription
msbarMutate a sequence
shuffleseqShuffles a set of sequences maintaining composition

B.6.32. Applications in group Protein:profiles

Table B.36. Applications in group Protein:profiles
ApplicationDescription
profitScan one or more sequences with a simple frequency matrix
prophecyCreate frequency matrix or profile from a multiple alignment
prophetScan one or more sequences with a Gribskov or Henikoff profile

B.6.33. Applications in group Utils:database creation

Table B.37. Applications in group Utils:database creation
ApplicationDescription
aaindexextractExtract amino acid property data from AAINDEX
cutgextractExtract codon usage tables from CUTG database
jaspextractExtract data from JASPAR
printsextractExtract data from PRINTS database for use by pscan
prosextractProcesses the PROSITE motif database for use by patmatmotifs
rebaseextractProcess the REBASE database for use by restriction enzyme applications
tfextractProcess TRANSFAC transcription factor database for use by tfscan

B.6.34. Applications in group Utils:database indexing

Table B.38. Applications in group Utils:database indexing
ApplicationDescription
dbiblastIndex a BLAST database
dbifastaIndex a fasta file database
dbiflatIndex a flat file database
dbigcgIndex a GCG formatted database
dbxfastaIndex a fasta file database using b+tree indices
dbxflatIndex a flat file database using b+tree indices
dbxgcgIndex a GCG formatted database using b+tree indices

B.6.35. Applications in group Utils:misc

Table B.39. Applications in group Utils:misc
ApplicationDescription
embossdataFind and retrieve EMBOSS data files
embossversionReports the current EMBOSS version number

B.6.36. Applications in group Distance matrix

Table B.40. Applications in group Distance matrix
ApplicationDescription
efitchFitch-Margoliash and Least-Squares Distance Methods
ekitschFitch-Margoliash method with contemporary tips
eneighborPhylogenies from distance matrix by N-J or UPGMA method
ffitchFitch-Margoliash and Least-Squares Distance Methods
fkitschFitch-Margoliash method with contemporary tips
fneighborPhylogenies from distance matrix by N-J or UPGMA method

B.6.37. Applications in group HMM

Table B.41. Applications in group HMM
ApplicationDescription
oalistatStatistics for multiple alignment files
ohmmalignAlign sequences with an HMM
ohmmbuildBuild HMM
ohmmcalibrateCalibrate a hidden Markov model
ohmmconvertConvert between HMM formats
ohmmemitExtract HMM sequences
ohmmfetchExtract HMM from a database
ohmmindexIndex an HMM database
ohmmpfamAlign single sequence with an HMM
ohmmsearchSearch sequence database with an HMM
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

B.6.38. Applications in group RNA folding

Table B.42. Applications in group RNA folding
ApplicationDescription
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

B.6.39. Applications in group Discrete characters

Table B.43. Applications in group Discrete characters
ApplicationDescription
ecliqueLargest clique program
edollopDollo and polymorphism parsimony algorithm
edolpennyPenny algorithm Dollo or polymorphism
efactorMultistate to binary recoding program
emixMixed parsimony algorithm
epennyPenny algorithm, branch-and-bound
fcliqueLargest clique program
fdollopDollo and polymorphism parsimony algorithm
fdolpennyPenny algorithm Dollo or polymorphism
ffactorMultistate to binary recoding program
fmixMixed parsimony algorithm
fmoveInteractive mixed method parsimony
fparsDiscrete character parsimony
fpennyPenny algorithm, branch-and-bound

B.6.40. Applications in group Tree drawing

Table B.44. Applications in group Tree drawing
ApplicationDescription
fdrawgramPlots a cladogram- or phenogram-like rooted tree diagram
fdrawtreePlots an unrooted tree diagram
fretreeInteractive tree rearrangement

B.6.41. Applications in group Menus

Table B.45. Applications in group Menus
ApplicationDescription
emnuSimple menu of EMBOSS applications

B.6.42. Applications in group Test

Table B.46. Applications in group Test
ApplicationDescription
crystalballAnswers every drug discovery question about a sequence
myseqDemonstration of sequence reading
mytestDemonstration of sequence reading

B.6.43. Applications in group Continuous characters

Table B.47. Applications in group Continuous characters
ApplicationDescription
econtmlContinuous character Maximum Likelihood method
econtrastContinuous character Contrasts
fcontrastContinuous character Contrasts

B.6.44. Applications in group Transcription

Table B.48. Applications in group Transcription
ApplicationDescription
tfscanScans DNA sequences for transcription factors

B.6.45. Applications in group Gene frequencies

Table B.49. Applications in group Gene frequencies
ApplicationDescription
egendistGenetic Distance Matrix program
fcontmlGene frequency and continuous character Maximum Likelihood
fgendistCompute genetic distances from gene frequencies

B.6.46. Applications in group Phylogeny:Consensus

Table B.50. Applications in group Phylogeny:Consensus
ApplicationDescription
econsenseMajority-rule and strict consensus tree
fconsenseMajority-rule and strict consensus tree
ftreedistDistances between trees
ftreedistpairDistances between two sets of trees