Bio::Tools::Phylo::Molphy - DESCRIPTION of Object use Bio::Tools::Phylo::Molphy; my $parser = new Bio::Tools::Phylo::Molphy(-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 = new Bio::TreeIO(-format => "newick"); $out->write_tree($trees[0]); # writing only the 1st tree } A parser for Molphy output (protml,dnaml)

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Tools::Phylo::Molphy(); 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