Reference

Bio::Tools::Run::Phylo::Raxml(3pm)

Bio::Tree getter from DNA alignment through raxml

NAME

Bio::Tools::Run::Phylo::Raxml - Bio::Tree getter from DNA alignment through 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.

  [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:

[email protected]

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 [email protected]

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

History