Biosequence analysis using profile hidden Markov models
HMMER is used for searching sequence databases for sequence homologs, and for
making sequence alignments. It implements methods using probabilistic models
called profile hidden Markov models (profile HMMs).
Version: 3.3.2
See also: hmmer-easel.
General Commands | |
| alimask | calculate and add column mask to a multiple sequence alignment |
| hmmalign | align sequences to a profile |
| hmmbuild | construct profiles from multiple sequence alignments |
| hmmc2 | example client for the HMMER daemon |
| hmmconvert | convert profile file to various formats |
| hmmemit | sample sequences from a profile |
| hmmer | profile HMMs for biological sequence analysis |
| hmmfetch | retrieve profiles from a file |
| hmmlogo | produce a conservation logo graphic from a profile |
| hmmpgmd | daemon for database search web services |
| hmmpgmd_shard | sharded daemon for database search web services |
| hmmpress | prepare a profile database for hmmscan |
| hmmscan | search sequence(s) against a profile database |
| hmmsearch | search profile(s) against a sequence database |
| hmmsim | collect profile score distributions on random sequences |
| hmmstat | summary statistics for a profile file |
| jackhmmer | iteratively search sequence(s) against a sequence database |
| makehmmerdb | build nhmmer database from a sequence file |
| nhmmer | search DNA queries against a DNA sequence database |
| nhmmscan | search DNA sequence(s) against a DNA profile database |
| phmmer | search protein sequence(s) against a protein sequence database |