NAME

       hmm_tweak - Alter transition probabilities in an HMM definition file.

DESCRIPTION

       Alter  transition  probabilities  in  an  HMM definition file.  After specified operations are performed,
       transition probabilities are renormalized and the adjusted file is written to standard out.  This program
       may be used multiple times in a pipe.

USAGE

       hmm_tweak [OPTIONS] <file.hmm> <cmap.cm>

OPTIONS

       -f <cats>
              Operate on transitions *from* states corresponding to the specified category names  (default  all)
              -t  <cats>  Operate  on  transitions  *to*  states  corresponding  to the specified category names
              (default all) -m <fact> Multiply transition probabilities by the specified factor.

       -a <const> Add the specified constant to transition probabilities.  -e <val> Set transition probabilities
              equal to the specified value.

       -i <icats> Assume a phylo-HMM indel model for states corresponding to

              the specified category names.  -u <tree> (Required with -i) Assume given tree topology (.nh file).
              -F <gps> (For use with  -i)  Operate  on  transitions  from  states  corresp.   to  the  specified
              gap-pattern numbers (ANDed with -f).

       -T <gps>
              (For  use with -i) Operate on transitions to states corresp.  to the specified gap-pattern numbers
              (ANDed with  -t).   -z  Equalize  transition  probabilities.   Set  all  transition  probabilities
              indicated  by  -f/-t/-F/-T  to  their  overall average value.  Options -m and/or -a can be used to
              adjust this average value.  -R Restrict to successive transitions within  a  category  range.   -y
              Like  -z,  except  compute  separate  averages  for  five classes of transitions, based on the gap
              patterns of the states involved: between null gap patterns, between equal non-null  gap  patterns,
              from  null  to  non-null gap patterns, from non-null to null gap patterns, and all others.  Useful
              with the indel model when training data is sparse (e.g., for splice-site states).  Options -m  and
              -a will be applied to transitions of the 3rd and 5th classes described.

       -h     Print this help message.

hmm_tweak 1.4                                       May 2016                                        HMM_TWEAK(1)