Bio::Tools::Run::Phylo::Molphy::ProtML - A wrapper for the Molphy pkg app ProtML use Bio::AlignIO; use Bio::TreeIO; use Bio::Tools::Run::Phylo::Molphy::ProtML; my %args = ( 'models' => 'jtt', 'search' => 'quick', "other" => [ '-information', '-w']); my $verbose = 0; # change to 1 if you want some debugging output my $protml = new Bio::Tools::Run::Phylo::Molphy::ProtML(-verbose => $verbose, -flags => \%args); die("cannot find the protml executable") unless $protml->executable; # read in a previously built protein alignment my $in = new Bio::AlignIO(-format => 'clustalw', -file => 't/data/cel-cbr-fam.aln'); my $aln = $in->next_aln; $protml->alignment($aln); my ($rc,$results) = $protml->run(); # This may be a bit of overkill, but it is possible we could # have a bunch of results and $results is a # Bio::Tools::Phylo::Molphy object my $r = $results->next_result; # $r is a Bio::Tools::Phylo::Molphy::Result object my @trees; while( my $t = $r->next_tree ) { push @trees, $t; } print "search space is ", $r->search_space, "\n"; "1st tree score is ", $tree[0]->score, "\n"; my $out = new Bio::TreeIO(-file => ">saved_MLtrees.tre", -format => "newick"); $out->write_tree($tree[0]); $out = undef; This is a wrapper for the exe from the Molphy (MOLecular PHYlogenetics) package by Jun Adachi & Masami Hasegawa. The software can be downloaded from http://www.ism.ac.jp/software/ismlib/softother.e.html or http://ftp.ism.ac.jp:8000/ISMLIB/MOLPHY/ websites. Note that the PHYLIP (Joe Felsenstein) also provides a version of the protml which this module is currently NOT prepared to handle. Use the package available directly from MOLPHY authors if you want to use the module in its present implementation, (extensions are welcomed!). The main components are the protml and nucml executables which are used to build maximum likelihood (ML) phylogenetic trees based on either protein or nucleotide sequences. Here are the valid input parameters, we have added a longhand version of the parameters to help you understand what each one does. Either the longhand or the original Molphy parameter will work. on the left while the Molphy parameter is on the Bioperl Molphy Description Longhand parameter Model (one of these): --------------- jtt j Jones, Taylor & Thornton (1992) jtt-f jf JTT w/ frequencies dayhoff d Dahoff et al. (1978) dayhoff-f d dayhoff w/ frequencies mtrev24 m mtREV24 Adachi & Hasegwa (1995) mtrev24-f mf mtREV24 w/ frequencies poisson p Poisson proportional pf Proportional rsr r Relative Substitution Rate rsr-f rf RSR w/ frequencies frequencies f data frequencies Search Strategy (one of these): ---------------- usertrees u User trees (must also supply a tree) rearrangement R Local rearrangement lbp RX Local boostrap prob exhaustive e Exhaustive search star s Star decomposition search (may not be ML) quick q Quick Add OTU search (may not be ML) distance D ML Distance matrix --> NJDIST (need to supply NJDIST tree) Others (can be some or all of these): --------------- norell-bp b No RELL-BP minimumevolution M Minimum evolution sequential S Sequence is in Sequential format _OR_ interleaved I Sequence is in Interleaved format verbose v Verbose messages directed to STDERR information i Output some information (tree vals) w More some extra information (transition matricies, etc)

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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 the web: 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 _

program_name
Title : program_name Usage : >program_name() Function: holds the program name Returns: string Args : None

program_dir
Title : program_dir Usage : ->program_dir() Function: returns the program directory, obtiained from ENV variable. Returns: string Args :

new
Title : new Usage : my $obj = new Bio::Tools::Run::Phylo::Molphy::ProtML(); Function: Builds a new Bio::Tools::Run::Phylo::Molphy::ProtML object Returns : Bio::Tools::Run::Phylo::Molphy::ProtML Args : -alignment => the Bio::Align::AlignI object -save_tempfiles => boolean to save the generated tempfiles and NOT cleanup after onesself (default FALSE) -tree => the Bio::Tree::TreeI object -params => a hashref of PAML parameters (all passed to set_parameter) -executable => where the protml executable resides See also: Bio::Tree::TreeI, Bio::Align::AlignI

run
Title : run Usage : $protml->run(); Function: run the protml analysis using the default or updated parameters the alignment parameter must have been set Returns : Bio::Tools::Phylo::Molphy Args :

alignment
Title : alignment Usage : $protml->align($aln); Function: Get/Set the Bio::Align::AlignI object Returns : Bio::Align::AlignI object Args : [optional] Bio::Align::AlignI Comment : We could potentially add support for running directly on a file but we shall keep it simple See also : L<Bio::SimpleAlign>, L<Bio::Align::AlignI>

tree
Title : tree Usage : $protml->tree($tree, %params); Function: Get/Set the Bio::Tree::TreeI object Returns : Bio::Tree::TreeI Args : [optional] $tree => Bio::Tree::TreeI, Comment : We could potentially add support for running directly on a file but we shall keep it simple See also : L<Bio::Tree::Tree>

get_flags
Title : get_flags Usage : my @params = $protml->get_flags(); Function: returns the list of flags Returns : array of flag names coded in the way that Args : none

set_flag
Title : set_flag Usage : $protml->set_parameter($type,$val); Function: Sets a protml parameter, will be validated against the valid values as set in the %VALIDVALUES class variable. The checks can be ignored if one turns off param checks like this: $protml->no_param_checks(1) Returns : boolean if set was success, if verbose is set to -1 then no warning will be reported Args : $type => name of the parameter This can be one of 'search', 'model', 'other' $value => flag value See also: L<no_param_checks()>

get_parameters
Title : get_parameters Usage : my %params = $protml->get_parameters(); Function: returns the list of parameters as a hash Returns : associative array keyed on parameter names Args : none

set_parameter
Title : set_parameter Usage : $protml->set_parameter($param,$val); Function: Sets a protml parameter, will be validated against the valid values as set in the %VALIDVALUES class variable. The checks can be ignored if one turns off param checks like this: $protml->no_param_checks(1) Returns : boolean if set was success, if verbose is set to -1 then no warning will be reported Args : $param => name of the parameter $value => value to set the parameter to See also: L<no_param_checks()>

no_param_checks
Title : no_param_checks Usage : $obj->no_param_checks($newval) Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values Returns : value of no_param_checks Args : newvalue (optional)

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

outfile_name
Title : outfile_name Usage : my $outfile = $protml->outfile_name(); Function: Get/Set the name of the output file for this run (if you wanted to do something special) Returns : string Args : [optional] string to set value to

tempdir
Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none

cleanup
Title : cleanup Usage : $protml->cleanup(); Function: Will cleanup the tempdir directory after a PAML run Returns : none Args : none

io
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none