hmm_tweak - Alter transition probabilities in an HMM definition
file.
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.
hmm_tweak [OPTIONS] <file.hmm> <cmap.cm>
- -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.