Bio::Tools::Run::Alignment::MAFFT - run the MAFFT alignment tools use Bio::Tools::Run::Alignment::MAFFT; You can get MAFFT from http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft4/ Basically fftnsi is the default in this implementation.

Mailing Lists
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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.open-bio.org/ Email jason-at-bioperl.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 : $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, obtiained from ENV variable. Returns: string Args :

error_string
Title : error_string Usage : $obj->error_string($newval) Function: Where the output from the last analysus 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

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