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# NAME

Bio::Tools::Phylo::Molphy::Result - container for data parsed from a ProtML run

# SYNOPSIS

``````  # do not use this object directly, you will get it back as part of a
# Molphy parser
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 container for data parsed from a ProtML run.

# 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``````

## Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

## 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:

``  https://github.com/bioperl/bioperl-live/issues``

# 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::Result->new();
Function: Builds a new Bio::Tools::Phylo::Molphy::Result object
Returns : Bio::Tools::Phylo::Molphy::Result
Args    : ``````

## model

`````` Title   : model
Usage   : \$obj->model(\$newval)
Function:
Returns : value of model
Args    : newvalue (optional)``````

## substitution_matrix

`````` Title   : substitution_matrix
Usage   : my \$smat = \$result->subsitution_matrix;
Function: Get the relative substitution matrix calculated in the ML procedure
Returns : reference to hash of hashes where key is the aa/nt name and value
is another hash ref which contains keys for all the aa/nt
possibilities
Args    : none``````

## transition_probability_matrix

`````` Title   : transition_probability_matrix
Usage   : my \$matrixref = \$molphy->transition_probablity_matrix();
Function: Gets the observed transition probability matrix
Returns : hash of hashes of aa/nt transition to each other aa/nt
Args    : Transition matrix type, typically
'1PAM-1.0e05' or '1PAM-1.0e07'``````

## residue_frequencies

`````` Title   : residue_frequencies
Usage   : my %data = \$molphy->residue_frequencies()
Function: Get the modeled and expected frequencies for
each of the residues in the sequence
Returns : hash of either aa (protml) or nt (nucml) frequencies
each key will point to an array reference where
1st slot is model's expected frequency
2nd slot is observed frequency in the data
\$hash{'A'}->[0] =
Args    : none``````

## next_tree

`````` Title   : next_tree
Usage   : my \$tree = \$factory->next_tree;
Function: Get the next tree from the factory
Returns : L<Bio::Tree::TreeI>
Args    : none``````

## rewind_tree

`````` Title   : rewind_tree_iterator
Usage   : \$result->rewind_tree()
Function: Rewinds the tree iterator so that next_tree can be
called again from the beginning
Returns : none
Args    : none``````

`````` Title   : add_tree
`````` Title   : search_space