++ed by:

11 PAUSE users
14 non-PAUSE users.

Christopher Fields
and 1 contributors

# NAME

Bio::Tools::Phylo::Molphy - parser for Molphy output

# SYNOPSIS

``````  use Bio::Tools::Phylo::Molphy;
my \$parser = Bio::Tools::Phylo::Molphy->new(-file => 'output.protml');
while( my \$r = \$parser->next_result ) {
# r is a Bio::Tools::Phylo::Molphy::Result object

# print the model name
print \$r->model, "\n";

# get the substitution matrix
# this is a hash of 3letter aa codes -> 3letter aa codes representing
# substitution rate
my \$smat = \$r->substitution_matrix;
print "Arg -> Gln substitution rate is %d\n",
\$smat->{'Arg'}->{'Gln'}, "\n";

# get the transition probablity matrix
# this is a hash of 3letter aa codes -> 3letter aa codes representing
# transition probabilty
my \$tmat = \$r->transition_probability_matrix;
print "Arg -> Gln transition probablity is %.2f\n",
\$tmat->{'Arg'}->{'Gln'}, "\n";

# get the frequency for each of the residues
my \$rfreqs = \$r->residue_frequencies;

foreach my \$residue ( keys %{\$rfreqs} ) {
printf "residue %s  expected freq: %.2f observed freq: %.2f\n",
\$residue,\$rfreqs->{\$residue}->[0], \$rfreqs->{\$residue}->[1];
}

my @trees;
while( my \$t = \$r->next_tree ) {
push @trees, \$t;
}

print "search space is ", \$r->search_space, "\n",
"1st tree score is ", \$trees[0]->score, "\n";

# writing to STDOUT, use -file => '>filename' to specify a file
my \$out = Bio::TreeIO->new(-format => "newick");
\$out->write_tree(\$trees[0]); # writing only the 1st tree
}``````

# DESCRIPTION

A parser for Molphy output (protml,dnaml)

# FEEDBACK

## Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

``````  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists``````

## Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

``  http://bugzilla.open-bio.org/``

# AUTHOR - Jason Stajich

Email jason-at-bioperl.org

# APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

## new

`````` Title   : new
Usage   : my \$obj = Bio::Tools::Phylo::Molphy->new();
Function: Builds a new Bio::Tools::Phylo::Molphy object
Returns : Bio::Tools::Phylo::Molphy
Args    : -fh/-file => \$val, # for initing input, see Bio::Root::IO``````

## next_result

`````` Title   : next_result
Usage   : my \$r = \$molphy->next_result
Function: Get the next result set from parser data
Returns : Bio::Tools::Phylo::Molphy::Result object
Args    : none``````