.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH HHMAKE "1" "November 2014" "hhmake 2.0.16" "User Commands"
.SH NAME
hhmake \- build an HMM from an input alignment or convert between HMMER format and HHsearch format
.SH SYNOPSIS
.B hhmake
\fI\,\-i file \/\fR[\fI\,options\/\fR]
.SH DESCRIPTION
HHmake version 2.0.16 (January 2013)
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
.TP
\fB\-i\fR <file>
query alignment (A2M, A3M, or FASTA), or query HMM
.SS "Output options:"
.TP
\fB\-o\fR <file>
HMM file to be written to  (default=<infile.hhm>)
.TP
\fB\-a\fR <file>
HMM file to be appended to
.TP
\fB\-v\fR <int>
verbose mode: 0:no screen output  1:only warings  2: verbose
.TP
\fB\-seq\fR <int>
max. number of query/template sequences displayed (def=10)
Beware of overflows! All these sequences are stored in memory.
.TP
\fB\-cons\fR
make consensus sequence master sequence of query MSA
.TP
\fB\-name\fR <name>
use this name for HMM (default: use name of first sequence)
.PP
Filter query multiple sequence alignment
.TP
\fB\-id\fR
[0,100]  maximum pairwise sequence identity (%) (def=90)
.TP
\fB\-diff\fR [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)
.TP
\fB\-cov\fR
[0,100]  minimum coverage with query (%) (def=0)
.TP
\fB\-qid\fR
[0,100]  minimum sequence identity with query (%) (def=0)
.TP
\fB\-qsc\fR
[0,100]  minimum score per column with query  (def=\-20.0)
.TP
\fB\-neff\fR [1,inf]
target diversity of alignment (default=off)
.SS "Input alignment format:"
.TP
\fB\-M\fR a2m
use A2M/A3M (default): upper case = Match; lower case = Insert;
\&'\-' = Delete; '.' = gaps aligned to inserts (may be omitted)
.TP
\fB\-M\fR first
use FASTA: columns with residue in 1st sequence are match states
.TP
\fB\-M\fR [0,100]
use FASTA: columns with fewer than X% gaps are match states
.SS "Pseudocount (pc) options:"
.TP
\fB\-pcm\fR
0\-2      position dependence of pc admixture 'tau' (pc mode, default=0)
.TP
0: no pseudo counts:
tau = 0
.TP
1: constant
tau = a
.IP
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
.TP
\fB\-pca\fR
[0,1]    overall pseudocount admixture (def=1.0)
.TP
\fB\-pcb\fR
[1,inf[  Neff threshold value for \fB\-pcm\fR 2 (def=1.5)
.TP
\fB\-pcc\fR
[0,3]    extinction exponent c for \fB\-pcm\fR 2 (def=1.0)
.TP
\fB\-pre_pca\fR [0,1]
PREFILTER pseudocount admixture (def=0.8)
.HP
\fB\-pre_pcb\fR [1,inf[ PREFILTER threshold for Neff (def=1.8)
.SS "Context\-specific pseudo\-counts:"
.TP
\fB\-nocontxt\fR
use substitution\-matrix instead of context\-specific pseudocounts
.HP
\fB\-contxt\fR <file> context file for computing context\-specific pseudocounts (default=./data/context_data.lib)
.TP
\fB\-cslib\fR
<file> column state file for fast database prefiltering (default=./data/cs219.lib)
.PP
Example: hhmake \fB\-i\fR test.a3m