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


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


         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,

         # combinations of files/ objects are possible

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


       This is a wrapper for running the Pal2Nal perl script by Mikita Suyama. You can get
       details here: 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 -

       You will need to enable this Pal2Nal wrapper to find the 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;


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AUTHOR - Sendu Bala



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

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

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

        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 can be supplied as key =>
                  value pairs.

                  These options can NOT be used with this wrapper:

        Title   : run
        Usage   : $result = $factory->run($protein_align_file, $multi_fasta_nucleotide);
                  $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
                  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.

        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