--- name: "Bio::Tools::Run::Phylo::Phylip::Consense" section: "3pm" platform: "linux" package: "libbio-perl-run-perl" version: "1.7.3-13" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Tools::Run::Phylo::Phylip::Consense" --- # Bio::Tools::Run::Phylo::Phylip::Consense(3pm) Wrapper for the phylip program Consense ## NAME Bio::Tools::Run::Phylo::Phylip::Consense - Wrapper for the phylip program Consense ## SYNOPSIS ``` use Bio::Tools::Run::Phylo::Phylip::Consense; use Bio::Tools::Run::Phylo::Phylip::SeqBoot; use Bio::Tools::Run::Phylo::Phylip::ProtDist; use Bio::Tools::Run::Phylo::Phylip::Neighbor; use Bio::Tools::Run::Phylo::Phylip::DrawTree; #first get an alignment my $aio= Bio::AlignIO->new(-file=>$ARGV[0],-format=>"clustalw"); my $aln = $aio->next_aln; # To prevent truncation of sequence names by PHYLIP runs, use set_displayname_safe my ($aln_safe, $ref_name)=$aln->set_displayname_safe(); #next use seqboot to generate multiple aligments my @params = ('datatype'=>'SEQUENCE','replicates'=>10); my $seqboot_factory = Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params); my $aln_ref= $seqboot_factory->run($aln); Or, for long sequence names: my $aln_ref= $seqboot_factory->run($aln_safe); #next build distance matrices and construct trees my $pd_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(); my $ne_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new(); foreach my $a (@{$aln_ref}){ my $mat = $pd_factory->create_distance_matrix($a); push @tree, $ne_factory->create_tree($mat); } #now use consense to get a final tree my $con_factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(); #you may set outgroup either by the number representing the order in #which species are entered or by the name of the species $con_factory->outgroup(1); $con_factory->outgroup('HUMAN'); my $tree = $con_factory->run(\@tree); # Restore original sequence names, after ALL phylip runs: my @nodes = $tree->get_nodes(); foreach my $nd (@nodes){ $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf; } #now draw the tree my $draw_factory = Bio::Tools::Run::Phylo::Phylip::DrawTree->new(); my $image_filename = $draw_factory->draw_tree($tree); ``` ## DESCRIPTION Wrapper for phylip consense program Taken from phylip documentation... CONSENSE reads a file of computer-readable trees and prints out (and may also write out onto a file) a consensus tree. At the moment it carries out a family of consensus tree methods called the M\[l\] methods (Margush and McMorris, 1981). These include strict consensus and majority rule consensus. Basically the consensus tree consists of monophyletic groups that occur as often as possible in the data. More documentation on using Consense and setting parameters may be found in the phylip package. VERSION Support This wrapper currently supports v3.5 of phylip. There is also support for v3.6 although this is still experimental as v3.6 is still under alpha release and not all functionalities maybe supported. ## PARAMETERS FOR Consense ### TYPE Title : TYPE Description : (optional)\ Only available in phylip v3.6 ``` This program supports 3 types of consensus generation MRe : Majority Rule (extended) Any set of species that appears in more than 50% of the trees is included. The program then considers the other sets of species in order of the frequency with which they have appeared, adding to the consensus tree any which are compatible with it until STRICT: A set of species must appear in all input trees to be included in the strict consensus tree. MR : A set of species is included in the consensus tree if it is present in more than half of the input trees. Ml : The user is asked for a fraction between 0.5 and 1, and the program then includes in the consensus tree any set of species that occurs among the input trees more than that fraction of then time. The Strict consensus and the Majority Rule consensus are extreme cases of the M[l] consensus, being for fractions of 1 and 0.5 respectively usage: my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-type=>"Ml 0.7"); Defaults to MRe ``` ### ROOTED ``` Title: ROOTED Description: (optional) toggles between the default assumption that the input trees are unrooted trees and the selection that specifies that the tree is to be treated as a rooted tree and not re-rooted. Otherwise the tree will be treated as outgroup-rooted and will be re-rooted automatically at the first species encountered on the first tree (or at a species designated by the Outgroup option) usage: my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-rooted=>1); Defaults to unrooted ``` ### OUTGROUP ``` Title : OUTGROUP Description : (optional) It is in effect only if the Rooted option selection is not in effect. The trees will be re-rooted with a species of your choosing. usage my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-outgroup=>2); Defaults to first species encountered. ``` ## 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* rather than to the module maintainer directly. Many experienced and reponsive experts 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 - Shawn Hoon Email shawnh@fugu-sg.org ## APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_ ### program\_name ``` Title : program_name Usage : $obj->program_name() Function: holds the program name Returns: string Args : None ``` ### program\_dir ``` Title : program_dir Usage : ->program_dir() Function: returns the program directory, obtained from ENV variable. Returns: string Args : ``` ### idlength ``` Title : idlength Usage : $obj->idlength ($newval) Function: Returns : value of idlength Args : newvalue (optional) ``` ### run ``` Title : run Usage : $inputfilename = 't/data/prot.treefile'; $tree= $Consense_factory->run($inputfilename); or $tree= $consense_factory->run(\@tree); Function: Create bootstrap sets of alignments Example : Returns : a L Args : either a file containing trees in newick format or an array ref of L Throws an exception if argument is not either a string (eg a filename) or a Bio::Tree::TreeI object. If argument is string, throws exception if file corresponding to string name can not be found. ``` ### \_run ``` Title : _run Usage : Internal function, not to be called directly Function: makes actual system call to Consense program Example : Returns : an array ref of Args : Name of a file containing a set of tree in newick format and a parameter string to be passed to Consense ``` ### \_setinput() ``` Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for Consense program Example : Returns : name of file containing a trees in newick format Args : an array ref of Bio::Tree::Tree object or input file name ``` ### names() ``` Title : names Usage : $tree->names(\%names) Function: get/set for a hash ref for storing names in matrix with rank as values. Example : Returns : hash reference Args : hash reference ``` ### \_setparams() ``` Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for Consense program Example : Returns : parameter string to be passed to Consense Args : name of calling object ``` ## Bio::Tools::Run::Wrapper 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 = $Consense->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 : $codeml->cleanup(); Function: Will cleanup the tempdir directory after a Consense run Returns : none Args : none ``` ### io ``` Title : io Usage : $obj->io($newval) Function: Gets a L object Returns : L Args : none ```