Provided by: hmmer2_2.3.2+dfsg-5_amd64 
NAME
HMMER - profile hidden Markov model software
SYNOPSIS
hmm2align
Align multiple sequences to a profile HMM.
hmm2build
Build a profile HMM from a given multiple sequence alignment.
hmm2calibrate
Determine appropriate statistical significance parameters for a profile HMM prior to doing
database searches.
hmm2convert
Convert HMMER profile HMMs to other formats, such as GCG profiles.
hmm2emit
Generate sequences probabilistically from a profile HMM.
hmm2fetch
Retrieve an HMM from an HMM database
hmm2index
Create a binary SSI index for an HMM database
hmm2pfam
Search a profile HMM database with a sequence (i.e., annotate various kinds of domains in the
query sequence).
hmm2search
Search a sequence database with a profile HMM (i.e., find additional homologues of a modeled
family).
DESCRIPTION
These programs use profile hidden Markov models (profile HMMs) to model the primary structure consensus
of a family of protein or nucleic acid sequences.
OPTIONS
All HMMER programs give a brief summary of their command-line syntax and options if invoked without any
arguments. When invoked with the single argument, -h (i.e., help), a program will report more verbose
command-line usage information, including rarely used, experimental, and expert options. -h will report
version numbers which are useful if you need to report a bug or problem to me.
Each HMMER program has its own man page briefly summarizing command line usage. There is also a user's
guide that came with the software distribution, which includes a tutorial introduction and more detailed
descriptions of the programs.
See http://hmmer.janelia.org/ for on-line documentation and the current HMMER release.
In general, no command line options should be needed by beginning users. The defaults are set up for
optimum performance in most situations. Options that are single lowercase letters (e.g. -a ) are
"common" options that are expected to be frequently used and will be important in many applications.
Options that are single uppercase letters (e.g. -B ) are usually less common options, but also may be
important in some applications. Options that are full words (e.g. --verbose ) are either rarely used,
experimental, or expert options. Some experimental options are only there for my own ongoing experiments
with HMMER, and may not be supported or documented adequately.
SEQUENCE FILE FORMATS
In general, HMMER attempts to read most common biological sequence file formats. It autodetects the
format of the file. It also autodetects whether the sequences are protein or nucleic acid. Standard
IUPAC degeneracy codes are allowed in addition to the usual 4-letter or 20-letter codes.
Unaligned sequences
Unaligned sequence files may be in FASTA, Swissprot, EMBL, GenBank, PIR, Intelligenetics, Strider,
or GCG format. These formats are documented in the User's Guide.
Sequence alignments
Multiple sequence alignments may be in CLUSTALW, SELEX, or GCG MSF format. These formats are
documented in the User's Guide.
ENVIRONMENT VARIABLES
For ease of using large stable sequence and HMM databases, HMMER looks for sequence files and HMM files
in the current working directory as well as in system directories specified by environment variables.
BLASTDB
Specifies the directory location of sequence databases. Example: /seqlibs/blast-db/. In
installations that use BLAST software, this environment variable is likely to already be set.
HMMERDB
Specifies the directory location of HMM databases. Example: /seqlibs/pfam/.