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 2.0.16 (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

       -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=./data/context_data.lib)

       -cslib
              <file> column state file for fast database prefiltering (default=./data/cs219.lib)

       Example: hhmake -i test.a3m