Provided by: libbio-perl-run-perl_1.7.3-3_all bug


       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}){

         # 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 orginal names
         # Step 2. Run PHYLIP programs:
         $aln_ref = $seq->run($aln_safe);            #  Use $aln_safe instead of $aln
         # Step 3. Retrieve orgininal names
         $aio = Bio::AlignIO->new(
                    -format=>"fasta");               #  FASTA output to view full names
         foreach my $ai(@{$aln_ref}){
                my $new_aln=$ai->restore_displayname($ref_name); #  Restore names


       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

       More documentation on using seqboot and setting parameters may be found in the phylip

       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.


       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

       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

                    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

         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

       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


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       participation is much appreciated.
                  - General discussion  - About the mailing lists

       Please direct usage questions or support issues to the mailing list:

       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
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       resolution.  Bug reports can be submitted via the web:

AUTHOR - Shawn Hoon



       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Title   : program_name
        Usage   : >program_name()
        Function: holds the program name
        Returns:  string
        Args    : None

        Title   : program_dir
        Usage   : ->program_dir()
        Function: returns the program directory, obtained from ENV variable.
        Returns:  string
        Args    :

        Title   : idlength
        Usage   : $obj->idlength ($newval)
        Returns : value of idlength
        Args    : newvalue (optional)

        Title   : run
        Usage   :
               $inputfilename = 't/data/prot.phy';
               $matrix= $seqboot_factory->run($inputfilename);
               $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.

        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

        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

        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

Bio::Tools::Run::Wrapper methods

        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)

        Title   : save_tempfiles
        Usage   : $obj->save_tempfiles($newval)
        Returns : value of save_tempfiles
        Args    : newvalue (optional)

        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

        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

        Title   : cleanup
        Usage   : $codeml->cleanup();
        Function: Will cleanup the tempdir directory after a SeqBoot run
        Returns : none
        Args    : none

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

perl v5.30.0                                2020-01-0Bio::Tools::Run::Phylo::Phylip::SeqBoot(3pm)