NAME

       hhmake - build an HMM from an input alignment or convert between HMMER format and HHsearch format

SYNOPSIS

       hhmake -i file [options]

DESCRIPTION

       HHmake  3.0.0  (15-03-2015) 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:
              Context specific hhm pseudocounts:

       -pc_hhm_contxt_mode {0,..,3}
              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)   3:   CSBlast   admixture:     tau   =
              a(1+b)/(Neff[i]+b) (Neff[i]: number of effective seqs in local MSA around column i)

       -pc_hhm_contxt_a
              [0,1]        overall pseudocount admixture (def=0.9)

       -pc_hhm_contxt_b
              [1,inf[      Neff threshold value for mode 2 (def=4.0)

       -pc_hhm_contxt_c
              [0,3]        extinction exponent c for mode 2 (def=1.0)

              Context  independent  hhm  pseudocounts  (used for templates; used for query if contxt file is not
              available):

       -pc_hhm_nocontxt_mode {0,..,3}
              position dependence of pc admixture 'tau' (pc mode, default=2)

       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)

       -pc_hhm_nocontxt_a
              [0,1]        overall pseudocount admixture (def=1.0)

       -pc_hhm_nocontxt_b
              [1,inf[      Neff threshold value for mode 2 (def=1.5)

       -pc_hhm_nocontxt_c
              [0,3]        extinction exponent c for mode 2 (def=1.0)

              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.crf)

   Other options:
       -maxres <int>
              max number of HMM columns (def=20001)

       Example: hhmake -i test.a3m

hhmake 3.0~beta2                                  January 2017                                         HHMAKE(1)