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Manual Reference Pages  -  BIO::TOOLS::RUN::ALIGNMENT::MAFFT (3)

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NAME

Bio::Tools::Run::Alignment::MAFFT - run the MAFFT alignment tools

CONTENTS

SYNOPSIS



  # Build a MAFFT alignment factory
  $factory = Bio::Tools::Run::Alignment::MAFFT->new(@params);

  # Pass the factory a list of sequences to be aligned.
  $inputfilename = t/cysprot.fa;
  # $aln is a SimpleAlign object.
  $aln = $factory->align($inputfilename);

  # or where @seq_array is an array of Bio::Seq objects
  $seq_array_ref = \@seq_array;
  $aln = $factory->align($seq_array_ref);

  #There are various additional options available.



DESCRIPTION

You can get MAFFT from <http://mafft.cbrc.jp/alignment/software/>. fftnsi is the default method for Mafft version 4 in this implementation.

See Bio::Tools::Run::Alignment::Clustalw for a description on how to specify parameters to the underlying alignment program. See the MAFFT manual page for a description of the MAFFT parameters.

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 one of the Bioperl mailing lists. Your participation is much appreciated.



  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/MailList.html - 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 the bugs and their resolution. Bug reports can be submitted via the web:



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



AUTHOR - Jason Stajich

Email jason-at-bioperl.org

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



    executable



 Title   : executable
 Usage   : my $exe = $blastfactory->executable(blastall);
 Function: Finds the full path to the codeml executable
 Returns : string representing the full path to the exe
 Args    : [optional] name of executable to set path to
           [optional] boolean flag whether or not warn when exe is not found



    program_path



 Title   : program_path
 Usage   : my $path = $factory->program_path();
 Function: Builds path for executable
 Returns : string representing the full path to the exe
 Args    : none



    program_dir



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



    error_string



 Title   : error_string
 Usage   : $obj->error_string($newval)
 Function: Where the output from the last analysis run is stored.
 Returns : value of error_string
 Args    : newvalue (optional)



    version



 Title   : version
 Usage   : exit if $prog->version() < 1.8
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none



    run



 Title   : run
 Usage   : my $output = $application->run(\@seqs);
 Function: Generic run of an application
 Returns : Bio::SimpleAlign object
 Args    : array ref of Bio::PrimarySeqI objects OR
           filename of sequences to run with



    align



 Title   : align
 Usage   :
    $inputfilename = t/data/cysprot.fa;
    $aln = $factory->align($inputfilename);
or
    $seq_array_ref = \@seq_array;
    # @seq_array is an array of Seq objs
    $aln = $factory->align($seq_array_ref);
 Function: Perform a multiple sequence alignment
 Returns : Reference to a SimpleAlign object containing the
           sequence alignment.
 Args    : Name of a file containing a set of unaligned fasta sequences
           or else an array of references to Bio::Seq objects.

 Throws an exception if argument is not either a string (eg a
 filename) or a reference to an array of Bio::Seq objects.  If
 argument is string, throws exception if file corresponding to string
 name can not be found. If argument is Bio::Seq array, throws
 exception if less than two sequence objects are in array.



    _run



 Title   :  _run
 Usage   :  Internal function, not to be called directly
 Function:  makes actual system call to tcoffee program
 Example :
 Returns : nothing; tcoffee output is written to a
           temporary file OR specified output file
 Args    : Name of a file containing a set of unaligned fasta sequences
           and hash of parameters to be passed to tcoffee



    _setinput



 Title   :  _setinput
 Usage   :  Internal function, not to be called directly
 Function:  Create input file for mafft programs
 Example :
 Returns : name of file containing mafft data input
 Args    : Seq or Align object reference or input file name



    _setparams



 Title   :  _setparams
 Usage   :  Internal function, not to be called directly
 Function:  Create parameter inputs for mafft program
 Example :
 Returns : parameter string to be passed to mafft program
 Args    : name of calling object



    methods



 Title   : methods
 Usage   : my @methods = $self->methods()
 Function: Get/Set Alignment methods - NOT VALIDATED
 Returns : array of strings
 Args    : arrayref of strings



    _version6



 Title   : _version6
 Usage   : Internal function, not to be called directly
 Function: Check if the version of MAFFT is 6
 Example :
 Returns : Boolean
 Args    : None



Bio::Tools::Run::BaseWrapper methods

    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 = $mafft->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   : $mafft->cleanup();
 Function: Will cleanup the tempdir directory
 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



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perl v5.20.3 BIO::TOOLS::RUN::ALIGNMENT::MAFFT (3) 2016-04-05

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