Bio::Tools::Run::Phylo::Phylip::SeqBoot - Wrapper for the phylip program SeqBoot #Create a SimpleAlign object @params = ('ktuple' => 2, 'matrix' => 'BLOSUM'); $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); $inputfilename = 't/data/cysprot.fa'; $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object. # Use seqboot to generate bootstap alignments my @params = ('datatype'=>'SEQUENCE','replicates'=>100); my $seq = Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params); my $aln_ref = $seq->run($aln); my $aio = Bio::AlignIO->new(-file=>">alignment.bootstrap",-format=>"phylip"); foreach my $ai(@{$aln_ref}){ $aio->write_aln($ai); } Wrapper for seqboot from the phylip package by Joseph Felsentein. Taken from phylip doc... "SEQBOOT is a general boostrapping tool. It is intended to allow you to generate multiple data sets that are resampled versions of the input data set. SEQBOOT can handle molecular sequences, binary characters, restriction sites, or gene frequencies." More documentation on using seqboot 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.

MODEL
Title : DATATYPE Description : (optional) This program supports 3 different datatypes SEQUENCE: Molecular Sequences MORPH : Discrete Morphological Characters REST : Restriction Sites GENEFREQ: Gene Frequencies Defaults to SEQUENCE

PERMUTE
Title: PERMUTE Description: (optional) 3 different resampling methods are available: BOOTSTRAP : creating a new data set by sampling N characters randomly with replacement The resulting data set has the same size as the original, but some characters have been left out and others are duplicated JACKKNIFE : Delete-half-jackknifing. It involves sampling a random half of the characters, and including them in the data but dropping the others The resulting data sets are half the size of the original, and no characters are duplicated. PERMUTE : Permuting species within characters. It involves permuting the columns of the data matrix separately. This produces data matrices that have the same number and kinds of characters but no taxonomic structure. Defaults to BOOTSTRAP

REPLICATES
Title : REPLICATES Description : (optional) This options allows the user to set the number of replicate data sets. Most statisticians would be happiest with 1000 to 10,000 replicates in a bootstrap, but 100 gives a good rough picture Defaults to 100

ALLELES
Title : ALLELES Description : (optional) This option is to be used with gene frequencies datatype option to specify that all alleles at each locus are in the input file. Defaults to NULL

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 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'; $matrix= $seqboot_factory->run($inputfilename); or $seq_array_ref = \@seq_array; @seq_array is array of Seq objs $aln = $clustalw_factory->align($seq_array_ref); $aln_ref = $SeqBootfactory->run($aln); Function: Create bootstrap sets of alignments Example : Returns : an array ref of L<Bio::SimpleAlign> 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 SeqBoot program Example : Returns : an array ref of <Bio::SimpleAlign> Args : Name of a file containing a set of multiple alignments in Phylip format and a parameter string to be passed to SeqBoot

_setinput()
Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for SeqBoot 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 SeqBoot program Example : Returns : parameter string to be passed to SeqBoot Args : name of calling object

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 = $SeqBoot->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 SeqBoot run Returns : none Args : none

io
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none