Package hmmer

Profile HMM software for protein sequence analysis

Profile hidden Markov models (profile HMMs) can be used to do sensitive
database searching using statistical descriptions of a sequence family's
consensus. HMMER is a freely distributable implementation of profile HMM
software for protein sequence analysis.

General Commands
Command Description
alimask Add mask line to a multiple sequence alignment
hmmalign align sequences to a profile HMM
hmmbuild construct profile HMM(s) from multiple sequence alignment(s)
hmmconvert convert profile file to a HMMER format
hmmemit sample sequences from a profile HMM
hmmer profile HMMs for biological sequence analysis
hmmfetch retrieve profile HMM(s) from a file
hmmlogo given an HMM, produce data required to build an HMM logo
hmmpgmd daemon for searching a protein query against a protein database
hmmpress prepare an HMM database for hmmscan
hmmscan search protein sequence(s) against a protein profile database
hmmsearch search profile(s) against a sequence database
hmmsim collect score distributions on random sequences
hmmstat display summary statistics for a profile file
jackhmmer iteratively search sequence(s) against a protein database
makehmmerdb build a HMMER binary database file from a sequence file
nhmmer search DNA/RNA queries against a DNA/RNA sequence database
nhmmscan search nucleotide sequence(s) against a nucleotide profile database
phmmer search protein sequence(s) against a protein sequence database