Hmmer
- alimask(1) calculate and add column mask to a multiple sequence alignment
- hmmalign(1) align sequences to a profile
- hmmbuild(1) construct profiles from multiple sequence alignments
- hmmc2(1) example client for the HMMER daemon
- hmmconvert(1) convert profile file to various formats
- hmmemit(1) sample sequences from a profile
- hmmer(1) profile HMMs for biological sequence analysis
- hmmfetch(1) retrieve profiles from a file
- hmmlogo(1) produce a conservation logo graphic from a profile
- hmmpgmd_shard(1) sharded daemon for database search web services
- hmmpgmd(1) daemon for database search web services
- hmmpress(1) prepare a profile database for hmmscan
- hmmscan(1) search sequence(s) against a profile database
- hmmsearch(1) search profile(s) against a sequence database
- hmmsim(1) collect profile score distributions on random sequences
- hmmstat(1) summary statistics for a profile file
- jackhmmer(1) iteratively search sequence(s) against a sequence database
- makehmmerdb(1) build nhmmer database from a sequence file
- nhmmer(1) search DNA queries against a DNA sequence database
- nhmmscan(1) search DNA sequence(s) against a DNA profile database
- phmmer(1) search protein sequence(s) against a protein sequence database