Package hmmer

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