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NAMEBio::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); DESCRIPTIONGet a Bio::Tree object using raxml given a protein or DNA alignment. FEEDBACKMailing ListsUser 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 SupportPlease 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 BugsReport 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 OsborneEmail briano@bioteam.net APPENDIXThe rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ newTitle : 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_nameTitle : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None program_dirTitle : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory Returns: string Args : error_stringTitle : 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) versionTitle : version Usage : exit if $prog->version() < 1.8 Function: Determine the version number of the program Example : Returns : float or undef Args : none quietTitle : quiet Usage : Function: get or set value for 'quiet' Example : Returns : Args : the value runTitle : 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). _runTitle : _run Usage : Internal function, not to be called directly Function: Runs the application Returns : Tree object Args : Alignment file name _write_alignfileTitle : _write_alignfile Usage : Internal function, not to be called directly Function: Create an alignment file Returns : filename Args : Bio::Align::AlignI _alphabetTitle : _alphabet Usage : my $alphabet = $self->_alphabet; Function: Get the alphabet of the input alignment, defaults to 'dna' Returns : 'dna' or 'protein' Args : Alignment file _setparamsTitle : _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 methodsno_param_checksTitle : no_param_checks Usage :
$obj->no_param_checks($newval) Function: Boolean
flag as to whether or not we should
save_tempfilesTitle : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional) outfile_nameTitle : outfile_name Usage : my $outfile =
$Raxml->outfile_name(); Function: Get/Set
the name of the output file for this run
tempdirTitle : 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 cleanupTitle : cleanup Usage : $Raxml->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none ioTitle : io Usage : $obj->io($newval) Function: Gets a Bio::Root::IO object Returns : Bio::Root::IO Args : none
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