--- name: "Bio::Tools::Run::Phylo::Phylip::ProtPars" 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::ProtPars" --- # Bio::Tools::Run::Phylo::Phylip::ProtPars(3pm) Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object 14 Nov 2002 Shawn Works with Phylip version 3.6 ## NAME Bio::Tools::Run::Phylo::Phylip::ProtPars - Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object 14 Nov 2002 Shawn Works with Phylip version 3.6 ## SYNOPSIS ``` #Create a SimpleAlign object @params = ('ktuple' => 2, 'matrix' => 'BLOSUM'); $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); $inputfilename = 't/data/cysprot.fa'; $aln = $factory->run($inputfilename); # $aln is a SimpleAlign object. #Create the Tree #using a threshold value of 30 and id name lengths limit of 30 #note to use id name length greater than the standard 10 in protpars, # you will need to modify the protpars source code $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars-> new(idlength=>30,threshold=>10,jumble=>"17,10",outgroup=>2); $tree = $tree_factory->run($aln); #Or one can pass in a file name containing a multiple alignment #in phylip format: $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(idlength=>30,threshold=>10); $tree = $tree_factory->run("/usr/users/shawnh/COMPARA/prot.phy"); # To prevent PHYLIP from truncating sequence names: # Step 1. Shelf the original names: my ($aln_safe, $ref_name)= # $aln_safe has serial names $aln->set_displayname_safe(); # $ref_name holds original names # Step 2. Run ProtPars: $tree = $protpars_factory->run($aln_safe); # Use $aln_safe instead of $aln # Step 3. Retrieve orgininal OTU names: use Bio::Tree::Tree; my @nodes=$tree->get_nodes(); foreach my $nd (@nodes){ $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf; } ``` ## PARAMTERS FOR PROTPARS COMPUTATION ### THRESHOLD Title : THRESHOLD Description : (optional)\ This sets a threshold such that if the number of\ steps counted in a character is higher than the\ threshold, it will be taken to be the threshold\ value rather than the actual number of steps. You\ should use a positive real number greater than 1.\ Please see the documetation from the phylip package\ for more information. ### OUTGROUP Title : OUTGROUP Description : (optional) ``` This specifies which species is to be used to root the tree by having it become the outgroup. Input values are integers specifying which species to use. Defaults to 1 ``` ### JUMBLE Title : JUMBLE Description : (optional)\ This enables you to tell the program to use a random\ number generator to choose the input order of\ species. Input values is of the format:\ seed,iterations eg 17,10 seed: an integer between 1\ and 32767 and of the form 4n+1 which means that it\ must give a remainder of 1 when divided by 4. Each\ different seed leads to a different sequence of\ addition of species. By simply changing the random\ number seed and re-running programs one can look for\ other, and better trees. iterations: For a value of\ 10, this will tell the program to try ten different\ orders of species in constructing the trees, and the\ results printed out will reflect this entire search\ process (that is, the best trees found among all 10\ runs will be printed out, not the best trees from\ each individual run). ## 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 ## CONTRIBUTORS Email jason-AT-bioperl\_DOT\_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 : >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.phy'; $tree = $factory->run($inputfilename); or $seq_array_ref = \@seq_array; @seq_array is array of Seq objs $aln = $factory->run($seq_array_ref); $tree = $treefactory->run($aln); Function: Create a protpars tree from a SimpleAlign object Example : Returns : L object Args : Name of a file containing a multiple alignment in Phylip format or an SimpleAlign object Throws an exception if argument is not either a string (eg a filename) or a Bio::SimpleAlign object. If argument is string, throws exception if file corresponding to string name can not be found. ``` ### create\_tree ``` Title : create_tree Usage : $inputfilename = 't/data/prot.phy'; $tree = $factory->create_tree($inputfilename); or $seq_array_ref = \@seq_array; @seq_array is array of Seq objs $aln = $factory->align($seq_array_ref); $tree = $treefactory->create_tree($aln); Function: Create a protpars tree from a SimpleAlign object Example : Returns : L object Args : Name of a file containing a multiple alignment in Phylip format or an SimpleAlign object Throws an exception if argument is not either a string (eg a filename) or a Bio::SimpleAlign 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 protpars program Example : Returns : Bio::Tree object Args : Name of a file containing a set of multiple alignments in Phylip format and a parameter string to be passed to protpars ``` ### \_setinput() ``` Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for protpars program Example : Returns : name of file containing a multiple alignment in Phylip format Args : SimpleAlign object reference or input file name ``` ### \_setparams() ``` Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for protpars program Example : Returns : parameter string to be passed to protpars Args : name of calling object ```