/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Phylo::Raxml

NAME

Bio::Tools::Run::Phylo::Raxml

SYNOPSIS

# Build a Raxml factory
$factory = Bio::Tools::Run::Phylo::Raxml->new(-p  => 100);

# Get an alignment
my $alignio = Bio::AlignIO->new(
      -format => 'fasta',
      -file   => '219877.cdna.fasta');
my $alnobj = $alignio->next_aln;

# Analyze the aligment and get a Tree
my $tree = $factory->run($alnobj);

DESCRIPTION

Get a Bio::Tree object using raxml given a protein or DNA alignment.

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 one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

Do not contact the module maintainer directly. Many experienced experts at bioperl-l 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 the bugs and their resolution. Bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Brian Osborne

Email briano@bioteam.net

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $treebuilder = Bio::Tools::Run::Phylo::Raxml->new();
Function: Constructor
Returns : Bio::Tools::Run::Phylo::Raxml
Args    : Same as those used to run raxml. For example:

$factory = Bio::Tools::Run::Phylo::Raxml->new(-p  => 100, -SSE3 => 1)

program_name

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

program_dir

Title   : program_dir
Usage   : $factory->program_dir(@params)
Function: returns the program directory
Returns:  string
Args    :

error_string

Title   : error_string
Usage   : $obj->error_string($newval)
Function: Where the output from the last analysus run is stored.
Returns : value of error_string
Args    : newvalue (optional)

version

Title   : version
Usage   : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args    : none

quiet

Title   : quiet
Usage   : 
Function: get or set value for 'quiet'
Example :
Returns : 
Args    : the value

run

Title   : run
Usage   : $factory->run($stockholm_file) OR
          $factory->run($align_object)
Function: Runs Raxml to generate a tree 
Returns : Bio::Tree::Tree object
Args    : File name for your input alignment in stockholm format, OR
          Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign).

_run

Title   : _run
Usage   : Internal function, not to be called directly
Function: Runs the application
Returns : Tree object
Args    : Alignment file name

_write_alignfile

Title   : _write_alignfile
Usage   : Internal function, not to be called directly
Function: Create an alignment file
Returns : filename
Args    : Bio::Align::AlignI

_alphabet

Title   : _alphabet
Usage   : my $alphabet = $self->_alphabet;
Function: Get the alphabet of the input alignment, defaults to 'dna'
Returns : 'dna' or 'protein'
Args    : Alignment file

_setparams

Title   :  _setparams
Usage   :  Internal function, not to be called directly    
Function:  Create parameter inputs for Raxml program
Example :
Returns : parameter string to be passed to Raxml
Args    : name of calling object

Bio::Tools::Run::BaseWrapper 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 = $Raxml->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 : $Raxml->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none

io

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