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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.