Bio::Tools::Phylo::Molphy(3) parser for Molphy output


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


A parser for Molphy output (protml,dnaml)


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AUTHOR - Jason Stajich



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


 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


 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