Bio::Tools::Run::Phylo::FastTree(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::FastTree(3pm) |
NAME
Bio::Tools::Run::Phylo::FastTree - Bio::Tree getter from DNA alignment
SYNOPSIS
# Build a FastTree factory $factory = Bio::Tools::Run::Phylo::FastTree->new(-quiet => 1, -fastest => 1); # Get an alignment my $alignio = Bio::AlignIO->new( -format => 'fasta', -file => '219877.cdna.fasta'); my $alnobj = $alignio->next_aln; # Analyze the aligment and get a Tree my $tree = $factory->run($alnobj);
DESCRIPTION
Get a Bio::Tree object given a protein or DNA alignment.
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/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
Do not contact the module maintainer directly. Many experienced experts at bioperl-l 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 - Brian Osborne
Email briano@bioteam.net
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new Usage : my $treebuilder = Bio::Tools::Run::Phylo::FastTree->new(); Function: Constructor Returns : Bio::Tools::Run::Phylo::FastTree Args : -outfile_name => $outname
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 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 : $factory->run($stockholm_file) OR $factory->run($align_object) Function: Runs FastTree to generate a tree Returns : Bio::Tree::Tree object Args : File name for your input alignment in stockholm format, OR Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign).
_run
Title : _run Usage : Internal function, not to be called directly Function: Runs the application Returns : Tree object Args : Alignment file name
_write_alignfile
Title : _write_alignfile Usage : Internal function, not to be called directly Function: Create an alignment file Returns : filename Args : Bio::Align::AlignI
_alphabet
Title : _alphabet Usage : my $alphabet = $self->_alphabet; Function: Get the alphabet of the input alignment, defaults to 'dna' Returns : 'dna' or 'protein' Args : Alignment file
_setparams
Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for FastTree program Example : Returns : parameter string to be passed to FastTree Args : name of calling object
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 = $FastTree->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 : $FastTree->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
2023-01-22 | perl v5.36.0 |