HMMER3

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. Each tool has different input and output requirements. Please see the documentation below. If your system supports POSIX threads, HMMER will start in multithreaded mode with a default of 3 threads (one master thread and two worker threads).

It consists of 18 tools, including:

Tool	Description
hmmbuild	build profile from input multiple alignment
hmmalign	make multiple sequence alignment using a profile
hmmsearch	search profile against sequence database
hmmscan	search sequence against profile database
hmmpress	prepare profile database for hmmscan
phmmer	search single sequence against sequence database
jackhmmer	iteratively search single sequence against database
nhmmer	search DNA query against DNA sequence database
nhmmerscan	search DNA sequence against a DNA profile database
hmmfetch	retrieve profiles from a profile file
hmmstat	show summary statistics for a profile file
hmmemit	generate sample sequences from a profile
hmmlogo	produce a conservation logo graphic from a profile
hmmconvert	convert between different profile file formats
hmmpgmd	search daemon for the HMMER website
hmmpgmd_shard	sharded search daemon for the HMMER website
makehmmerdb	prepare an nhmmer binary database
hmmsim	collect score distributions on random sequences
alimask	add column mask to a multiple sequence alignment

tip

Several other tools load with this module. Review additional available tools using the command below:

report_subtools.sh hmmer

For additional information and running examples see the HMMER3 documentation

Parallel Capabilities: Multithreading options supported.