| Bio::Tools::Run::Phylo::Raxml(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::Raxml(3pm) |
Bio::Tools::Run::Phylo::Raxml - Bio::Tree getter from DNA alignment through 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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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.
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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
| 2023-01-22 | perl v5.36.0 |