hhmake(1) [debian man page]
HHMAKE(1) User Commands HHMAKE(1) NAME
hhmake - build an HMM from an input alignment or convert between HMMER format and HHsearch format SYNOPSIS
hhmake -i file [options] DESCRIPTION
HHmake version 2.0.15 (June 2012) Build an HMM from an input alignment in A2M, A3M, or FASTA format, or convert between HMMER format (.hmm) and HHsearch format (.hhm). Remmert M, Biegert A, Hauser A, and Soding J. HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9:173-175 (2011). (C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser -i <file> query alignment (A2M, A3M, or FASTA), or query HMM Output options: -o <file> HMM file to be written to (default=<infile.hhm>) -a <file> HMM file to be appended to -v <int> verbose mode: 0:no screen output 1:only warings 2: verbose -seq <int> max. number of query/template sequences displayed (def=10) Beware of overflows! All these sequences are stored in memory. -cons make consensus sequence master sequence of query MSA -name <name> use this name for HMM (default: use name of first sequence) Filter query multiple sequence alignment -id [0,100] maximum pairwise sequence identity (%) (def=90) -diff [0,inf[ filter MSA by selecting most diverse set of sequences, keeping at least this many seqs in each MSA block of length 50 (def=100) -cov [0,100] minimum coverage with query (%) (def=0) -qid [0,100] minimum sequence identity with query (%) (def=0) -qsc [0,100] minimum score per column with query (def=-20.0) -neff [1,inf] target diversity of alignment (default=off) Input alignment format: -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' = gaps aligned to inserts (may be omitted) -M first use FASTA: columns with residue in 1st sequence are match states -M [0,100] use FASTA: columns with fewer than X% gaps are match states Pseudocount (pc) options: -pcm 0-2 position dependence of pc admixture 'tau' (pc mode, default=0) 0: no pseudo counts: tau = 0 1: constant tau = a 2: diversity-dependent: tau = a/(1 + ((Neff[i]-1)/b)^c) (Neff[i]: number of effective seqs in local MSA around column i) 3: constant diversity pseudocounts -pca [0,1] overall pseudocount admixture (def=1.0) -pcb [1,inf[ Neff threshold value for -pcm 2 (def=1.5) -pcc [0,3] extinction exponent c for -pcm 2 (def=1.0) -pre_pca [0,1] PREFILTER pseudocount admixture (def=0.8) -pre_pcb [1,inf[ PREFILTER threshold for Neff (def=1.8) Context-specific pseudo-counts: -nocontxt use substitution-matrix instead of context-specific pseudocounts -contxt <file> context file for computing context-specific pseudocounts (default=debian/tmp/usr/share/hhsuite/data/context_data.lib) -cslib <file> column state file for fast database prefiltering (default=debian/tmp/usr/share/hhsuite/data/cs219.lib) Example: hhmake -i test.a3m hhmake 2.0.15 June 2012 HHMAKE(1)
Check Out this Related Man Page
hmmemit(1) HMMER Manual hmmemit(1) NAME
hmmemit - sample sequences from a profile HMM SYNOPSIS
hmmemit [options] hmmfile DESCRIPTION
The hmmemit program samples (emit) sequences from the profile HMM in hmmfile, and outputs them. The hmmfile should contain only a single HMM, not a library of them; only the first HMM will be read. The default is to sample a sequence sequence from the core probability model. Sampling sequences may be useful for a variety of purposes, including creating synthetic true positives for benchmarks or tests. COMMON OPTIONS
-h Help; print a brief reminder of command line usage and all available options. -c Emit a consensus sequence, instead of sampling a sequence from the profile HMM's probability distribution. The consensus sequence is formed by selecting the maximum probability residue at each match state. -o <f> Direct the output sequences to file <f>, rather than to stdout. -p Sample sequences from the implicit profile, not from the core model. The core model consists only of the homologous states (between the begin and end states of a HMMER Plan7 model). The profile includes the nonhomologous N, C, and J states, local/glocal and uni/multihit algorithm configuration, and the target length model. Therefore sequences sampled from a profile may include nonhomol- ogous as well as homologous sequences, and may contain more than one homologous sequence segment. By default, the profile is in mul- tihit local mode, and the target sequence length is configured for L=400. To change these defaults, see Options Controlling Emission from Profiles, below. -N <n> Sample <n> sequences, rather than just one. OPTIONS CONTROLLING EMISSION FROM PROFILES
All these options require that the -p option is also set. -L <n> Configure the profile's target sequence length model to generate a mean length of approximately <n> rather than the default of 400. --local Configure the profile for multihit local alignment. --unilocal Configure the profile for unihit local alignment (Smith/Waterman). --glocal Configure the profile for multihit glocal alignment. --uniglocal Configure the profile for unihit glocal alignment. OTHER OPTIONS
--seed <n> Seed the random number generator with <n>, an integer >= 0. If <n> is nonzero, any stochastic simulations will be reproducible; the same command will give the same results. If <n> is 0, the random number generator is seeded arbitrarily, and stochastic simulations will vary from run to run of the same command. The default is 0: use an arbitrary seed, so different hmmemit runs will generate different samples. SEE ALSO
See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package. For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (@HMMER_URL@). COPYRIGHT
@HMMER_COPYRIGHT@ @HMMER_LICENSE@ For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@). AUTHOR
Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org HMMER
@HMMER_VERSION@ @HMMER_DATE@ hmmemit(1)