NAME

       Bio::Tools::Run::Alignment::Pal2Nal - Wrapper for Pal2Nal

SYNOPSIS

         use Bio::Tools::Run::Alignment::Pal2Nal;

         # Make a Pal2Nal factory
         $factory = Bio::Tools::Run::Alignment::Pal2Nal->new();

         # Run Pal2Nal with a protein alignment file and a multi-fasta nucleotide
         # file
         my $aln = $factory->run($protein_alignfilename, $nucleotide_filename);

         # or with Bioperl objects
         $aln = $factory->run($protein_bio_simplalign, [$nucleotide_bio_seq1,
                                                        $nucleotide_bio_seq2]);

         # combinations of files/ objects are possible

         # $aln isa Bio::SimpleAlign of the nucleotide sequences aligned according to
         # the protein alignment

DESCRIPTION

       This is a wrapper for running the Pal2Nal perl script by Mikita Suyama. You can get
       details here: http://coot.embl.de/pal2nal/. Pal2Nal is used for aligning a set of
       nucleotide sequences based on an alignment of their translations.

       You can try supplying normal pal2nal command-line arguments to new(), eg.  new() or
       calling arg-named methods (excluding the initial hyphen, eg.  $factory->(1) to set the -
       arg).

       You will need to enable this Pal2Nal wrapper to find the pal2nal.pl script.  This can be
       done in (at least) three ways:

        1. Make sure the script is in your path.
        2. Define an environmental variable PAL2NALDIR which is a
           directory which contains the script:
           In bash:

           export PAL2NALDIR=/home/username/pal2nal/

           In csh/tcsh:

           setenv PAL2NALDIR /home/username/pal2nal

        3. Include a definition of an environmental variable PAL2NALDIR in
           every script that will use this Pal2Nal wrapper module, e.g.:

           BEGIN { $ENV{PAL2NALDIR} = '/home/username/pal2nal/' }
           use Bio::Tools::Run::Alignment::Pal2Nal;

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 the Bioperl mailing list.  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 of the bugs and their
       resolution. Bug reports can be submitted via the web:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala

       Email bix@sendu.me.uk

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   : $factory>program_name()
        Function: holds the program name
        Returns : string
        Args    : None

   program_dir
        Title   : program_dir
        Usage   : $factory->program_dir(@params)
        Function: returns the program directory, obtained from ENV variable.
        Returns : string
        Args    : None

   new
        Title   : new
        Usage   : $factory = Bio::Tools::Run::Alignment::Pal2Nal->new()
        Function: creates a new Pal2Nal factory.
        Returns : Bio::Tools::Run::Alignment::Pal2Nal
        Args    : Most options understood by pal2nal.pl can be supplied as key =>
                  value pairs.

                  These options can NOT be used with this wrapper:
                  -output
                  -html
                  -h
                  -nostderr

   run
        Title   : run
        Usage   : $result = $factory->run($protein_align_file, $multi_fasta_nucleotide);
                  -or-
                  $result = $factory->run($prot_align_object, [$bioseq_object1, ...]);
        Function: Runs pal2nal on a protein alignment and set of nucleotide sequences.
        Returns : Bio::SimpleAlign;
        Args    : The first argument represents a protein alignment, the second
                  argument a set of nucleotide sequences.
                  The alignment can be provided as an alignment file readable by
                  Bio::AlignIO, or a Bio::Align::AlignI compliant object (eg. a
                  Bio::SimpleAlign).
                  The nucleotide sequences can be provided as a single filename of a
                  fasta file containing multiple nucleotide sequences, or an array ref
                  of filenames, each file containing one sequence. Alternatively, an
                  array ref of Bio::PrimarySeqI compliant objects can be supplied.

                  In all cases, the protein alignment sequence names must correspond to
                  the names of the supplied nucleotide sequences.

   _setparams
        Title   : _setparams
        Usage   : Internal function, not to be called directly
        Function: Creates a string of params to be used in the command string
        Returns : string of params
        Args    : alignment and tree file names