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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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

add_tree

 Title   : add_tree
 Usage   : $result->add_tree($tree);
 Function: Adds a tree 
 Returns : integer which is the number of trees stored
 Args    : L<Bio::Tree::TreeI>

search_space

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