SYNOPSIS
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 = Bio::Tools::Run::Phylo::Molphy::ProtML->new(-verbose => $verbose,
-flags => \%args);
die("cannot find the protml executable") unless $protml->executable;
# read in a previously built protein alignment
my $in = Bio::AlignIO->new(-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 = Bio::TreeIO->new(-file => ">saved_MLtrees.tre",
-format => "newick");
$out->write_tree($tree[0]);
$out = undef;
DESCRIPTION
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/ismlib/softother.e.html>. Note that PHYLIP (Joe Felsenstein) also provides a version of 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.
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)
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-AT-bioperl_DOT_orgCONTRIBUTORS
Additional contributors names and emails hereAPPENDIX
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, obtained from ENV variable. Returns: string Args :
new
Title : new
Usage : my $obj = Bio::Tools::Run::Phylo::Molphy::ProtML->new();
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()>
Bio::Tools::Run::WrapperBase methods
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