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 #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");

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).

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://bio.perl.org/MailList.html - About the mailing lists

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://bugzilla.bioperl.org/ Email shawnh@fugu-sg.org Email jason@bioperl.org 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, obtiained 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<Bio::Tree> 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<Bio::Tree> 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