Commands in H4

H4 has a single executable, hmmer, which takes a <command> as its first option:

   % hmmer <command> [<options>] [<args..>]

The commands, and their HMMER3 analogs:

command	description	H3 analog
help	show help and usage info	<program> --help
version	show version info	<program> --version

| | build | build a protein model | hmmbuild | | palign | align protein sequences to protein profile | hmmalign | nalign | align DNA sequences to DNA profile | hmmalign | talign | align DNA sequences to protein profile | galign | align genomic seqs to protein profile | | psearch | seq database search: protein->protein | hmmsearch, phmmer, jackhmmer | nsearch | seq database search: DNA->DNA | nhmmer | tsearch | seq database search: protein->DNA | | gsearch | seq database search: protein->genome | | | pscan | profile database search: protein->protein | hmmscan | nscan | profile database search: DNA->DNA | nhmmscan | tscan | profile database search: DNA->protein | gscan | profile database search: genomic->protein | | daemon | search daemon | hmmpgmd | | compare | profile/profile comparison | | sample | sample sequences from a profile | hmmemit | logo | make a graphical logo from a profile | hmmlogo | | apress | index, compress alignment database | esl-afetch --index | mpress | index, compress profile database | hmmpress | spress | index, compress sequence database | esl-sfetch --index; esl_dsqdata_example | | afetch | fetch alignment from alignment database | esl-afetch | mfetch | fetch profile from profile database | hmmfetch | sfetch | fetch sequence from sequence database | esl-sfetch | | astat | show statistics for alignment database | esl-alistat | mstat | show statistics for profile database | hmmstat | sstat | show statistics for sequence database | esl-seqstat | | aconvert | convert alignment(s) to another format | esl-reformat | mconvert | convert profile(s) to another format | hmmconvert | sconvert | convert sequence(s) to another format | esl-reformat

A prefix of p, n, t, or g on a search/align program indicates protein/protein, nucleic/nucleic, translated nucleic/protein, and genomic (gene structure+translated)/protein comparison.

A prefix of a, m, or s on a dataset program indicates a dataset of alignments, models (profiles), or single sequences.

Some standardized options:

option	description	applies to commands
-J <n>	iterative search	*search
-S	query is a single sequence	*search
-A	query is a multiple alignment	*search; *compare