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.
alimask alimask is used to apply a mask line to a multiple sequence alignment, based on provided alignment or model coordinates. When hmmbuild receives a masked... hmmalign Perform a multiple sequence alignment of all the sequences in <seqfile> by aligning them individually to the profile HMM in <hmmfile>. The new alignment is... hmmbuild For each multiple sequence alignment in <msafile> build a profile HMM and save it to a new file <hmmfile_out>. <msafile> may be '-' (dash), which means reading... hmmconvert The hmmconvert utility converts an input profile file to different HMMER formats. By default, the input profile can be in any HMMER format, including... hmmemit The hmmemit program samples (emits) sequences from the profile HMM(s) in hmmfile, and writes them to output. Sampling sequences may be useful for a variety of... hmmer HMMER is a suite of several programs for biological sequence alignment and database homology search. It uses probabilistic models called "profile hidden Markov... hmmfetch Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam database, for example). For maximum speed, the <hmmfile> should be indexed first... hmmlogo hmmlogo computes letter height and indel parameters that can be used to produce a profile HMM logo. This tool is essentially a command-line interface for much... hmmpgmd The hmmpgmd program is the daemon that we use internally for the hmmer.org web server, and essentially stands in front of the protein search programs phmmer... hmmpress Starting from a profile database <hmmfile> in standard HMMER3 format, construct binary compressed datafiles for hmmscan. The hmmpress step is required for... hmmscan hmmscan is used to search protein sequences against collections of protein profiles. For each sequence in <seqfile>, use that query sequence to search the... hmmsearch hmmsearch is used to search one or more profiles against a sequence database. For each profile in <hmmfile>, use that query profile to search the target... hmmsim The hmmsim program generates random sequences, scores them with the model(s) in <hmmfile>, and outputs various sorts of histograms, plots, and fitted... hmmstat The hmmstat utility prints out a tabular file of summary statistics for each profile in <hmmfile>. <hmmfile> may be '-' (a dash character), in which case... jackhmmer jackhmmer iteratively searches each query sequence in <seqfile> against the target sequence(s) in <seqdb>. The first iteration is identical to a phmmer search... makehmmerdb makehmmerdb is used to create a binary file from a DNA sequence file. This binary file may be used as a target database for the DNA search tool... nhmmer nhmmer is used to search one or more nucleotide queries against a nucleotide sequence database. For each query in <queryfile>, use that query to search the... nhmmscan nhmmscan is used to search nucleotide sequences against collections of nucleotide profiles. For each sequence in <seqfile>, use that query sequence to search... phmmer phmmer is used to search one or more query protein sequences against a protein sequence database. For each query sequence in <seqfile>, use that sequence to...