| Bio::Tools::Run::Phylo::Raxml(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::Raxml(3pm) |
Bio::Tools::Run::Phylo::Raxml
# 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);
Get a Bio::Tree object using raxml given a protein or DNA alignment.
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Please direct usage questions or support issues to the mailing list:
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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.
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:
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Email briano@bioteam.net
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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)
Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory Returns: string Args :
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)
Title : version Usage : exit if $prog->version() < 1.8 Function: Determine the version number of the program Example : Returns : float or undef Args : none
Title : quiet Usage : Function: get or set value for 'quiet' Example : Returns : Args : the value
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).
Title : _run Usage : Internal function, not to be called directly Function: Runs the application Returns : Tree object Args : Alignment file name
Title : _write_alignfile Usage : Internal function, not to be called directly Function: Create an alignment file Returns : filename Args : Bio::Align::AlignI
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
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
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)
Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)
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
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
Title : cleanup Usage : $Raxml->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none
Title : io Usage : $obj->io($newval) Function: Gets a Bio::Root::IO object Returns : Bio::Root::IO Args : none
| 2018-09-14 | perl v5.26.2 |