| Cbstools |
| echlorop | Reports presence of chloroplast transit peptides |
| elipop | Prediction of lipoproteins |
| enetnglyc | Reports N-glycosylation sites in human proteins |
| enetoglyc | Reports mucin type GalNAc O-glycosylation sites in mammalian proteins |
| enetphos | Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins |
| eprop | Reports propeptide cleavage sites in proteins |
| esignalp | Reports protein signal cleavage sites |
| etmhmm | Reports transmembrane helices |
| eyinoyang | Reports O-(beta)-GlcNAc attachment sites |
| Domainatrix |
| cathparse | Generates DCF file from raw CATH files |
| domainnr | Removes redundant domains from a DCF file |
| domainreso | Remove low resolution 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 |
| Domalign |
| allversusall | Sequence similarity data from all-versus-all comparison |
| 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) |
| Domsearch |
| seqfraggle | Removes fragment sequences from DHF files |
| seqnr | Removes redundancy 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 |
| Emnu |
| emnu | Simple menu of EMBOSS applications |
| Esim4 |
| esim4 | Align an mRNA to a genomic DNA sequence |
| Hmmernew |
| 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 |
| Iprscan |
| eiprscan | Motif detection |
| Memenew |
| emast | Motif detection |
| ememe | Multiple EM for Motif Elicitation |
| ememetext | Multiple EM for Motif Elicitation. Text file only |
| Mira |
| emira | MIRA fragment assembly program |
| emiraest | MIRAest fragment assembly program |
| Mse |
| mse | Multiple Sequence Editor |
| Myembossdemo |
| Phylipnew |
| fclique | Largest clique program |
| fconsense | Majority-rule and strict consensus tree |
| fcontml | Gene frequency and continuous character Maximum Likelihood |
| fcontrast | Continuous character Contrasts |
| 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 |
| fdollop | Dollo and polymorphism parsimony algorithm |
| fdolmove | Interactive Dollo or Polymorphism Parsimony |
| fdolpenny | Penny algorithm Dollo or polymorphism |
| fdrawgram | Plots a cladogram- or phenogram-like rooted tree diagram |
| fdrawtree | Plots an unrooted tree diagram |
| ffactor | Multistate to binary recoding program |
| ffitch | Fitch-Margoliash and Least-Squares Distance Methods |
| ffreqboot | Bootstrapped genetic frequencies algorithm |
| fgendist | Compute genetic distances from gene frequencies |
| fkitsch | Fitch-Margoliash method with contemporary tips |
| fmix | Mixed parsimony algorithm |
| fmove | Interactive mixed method parsimony |
| fneighbor | Phylogenies from distance matrix by N-J or UPGMA method |
| fpars | Discrete character parsimony |
| fpenny | Penny algorithm, branch-and-bound |
| 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 |
| fretree | Interactive tree rearrangement |
| fseqboot | Bootstrapped sequences algorithm |
| fseqbootall | Bootstrapped sequences algorithm |
| ftreedist | Distances between trees |
| ftreedistpair | Distances between two sets of trees |
| Signature |
| 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 | Generates ligand-binding signatures from a CON file |
| sigscan | Generates hits (DHF file) from a signature search |
| sigscanlig | Searches ligand-signature library and writes hits (LHF file) |
| Structure |
| contacts | Generate intra-chain CON files from CCF files |
| domainer | Generates domain CCF files from protein CCF files |
| hetparse | Converts heterogen group dictionary to EMBL-like format |
| interface | Generate inter-chain CON files from CCF files |
| pdbparse | Parses 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 |
| Topo |
| topo | Draws an image of a transmembrane protein |
| Vienna |
| 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 |