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