Bio::Tools::Phylo::Molphy::Result - DESCRIPTION of Object # do not use this object directly, you will get it back as part of a # Molphy parser 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 container for data parsed from a ProtML run.

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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 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::Result(); 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)