Bio::Tools::Run::PiseApplication::drawtree.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::PiseApplication::drawtree

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::drawtree
       Bioperl class for:
 
         Phylip  drawtree - Plots an unrooted tree diagram (Felsenstein)
 
         References:
 
                 Felsenstein, J.  1993.  PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author.  Department of Genetics, University of Washington, Seattle.
 
                 Felsenstein, J.  1989.  PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics  5: 164-166.
 
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/drawtree.html 
          for available values):
 
 
                 drawtree (String)
 
                 treefile (InFile)
                         Tree File
                         pipe: phylip_tree
 
                 screen_type (String)
 
                 plotter (Excl)
                         Which plotter or printer will the tree be drawn on
 
                 xxres (Float)
                         X resolution
 
                 xyres (Float)
                         Y resolution
 
                 laserjet_resolution (Excl)
                         Laserjet resolution
 
                 pcx_resolution (Excl)
                         Paintbrush PCX resolution
 
                 preview (String)
 
                 branch_lengths (Switch)
                         Use branch lengths
 
                 angle (Excl)
                         Angle of labels
 
                 fixed_angle (Float)
                         Fixed angle: Are the labels to be plotted vertically (90), horizontally (0), or downwards (-90)? 
 
                 rotation (Float)
                         Rotation of tree (in degrees from 360 to -360)
 
                 arc (Float)
                         Angle of arc for tree (in degrees from 0 to 360)
 
                 iterate (Excl)
                         Iterate to improve tree
 
                 scale (Float)
                         Scale of branch length (default: Automatically rescaled)
 
                 horizontal_margins (Float)
                         Horizontal margins
 
                 vertical_margins (Float)
                         Vertical margins
 
                 character_height (Float)
                         Relative character height
 
                 font (String)
                         Font (PostScript only)
 
                 tops (String)
 
                 topict (String)
 
                 toxbm (String)
 
                 confirm (String)
 
 

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
 
 

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://bugzilla.open-bio.org/
 
 

AUTHOR

Catherine Letondal (letondal@pasteur.fr) Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided ``as is'' without warranty of any kind.

SEE ALSO

http://bioweb.pasteur.fr/seqanal/interfaces/drawtree.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

  Title   : new()
  Usage   : my $drawtree = Bio::Tools::Run::PiseApplication::drawtree->new($location, $email, @params);
  Function: Creates a Bio::Tools::Run::PiseApplication::drawtree object.
            This method should not be used directly, but rather by 
            a Bio::Tools::Run::AnalysisFactory::Pise instance.
            my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
            my $drawtree = $factory->program('drawtree');
  Example : -
  Returns : An instance of Bio::Tools::Run::PiseApplication::drawtree.