Bio::T...:newick(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 Bio::TreeIO::newick — parsing and writing of Newick/PHYLIP/New Hampshire format 💖

okay bestie, welcome to Bio::TreeIO::newick (that's the 3pm page, you're in the right place 🫶). This is the little module that handles parsing and writing of the Newick/PHYLIP/New Hampshire format. Tree stuff. Phylogenetics. Very science, very slay. 🌳✨

✨ SYNOPSIS ✨

# do not use this module directly
use Bio::TreeIO;

my $treeio = Bio::TreeIO->new(-format => 'newick',
                             -file => 't/data/LOAD_Ccd1.dnd');
my $tree = $treeio->next_tree;
🚨 bestie READ THE COMMENT: do not use this module directly. You go through Bio::TreeIO, okay? That's the whole vibe. 💅

🌸 DESCRIPTION 🌸

This module handles parsing and writing of Newick/PHYLIP/New Hampshire format. That's it, that's the job, and it does it gorgeously. 👑

🦋 FEEDBACK 🦋

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules, no cap. Send your comments and suggestions preferably to the Bioperl mailing list — your participation is much appreciated, fr fr. 🥹

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

...rather than to the module maintainer directly. Like, respectfully, don't DM the maintainer. 💀 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 — receipts help everybody.

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution (the way that we track and *resolve*… obsessed 🎀). Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

👑 AUTHOR - Jason Stajich 👑

Email jason-at-bioperl-dot-org

(iconic. legendary. the blueprint. 🌟)

🌈 APPENDIX 🌈

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

⭐ new

  • Title : new
  • Args :
    • -print_count => boolean, default is false
    • -bootstrap_style => set the bootstrap style (one of nobranchlength, molphy, traditional)
    • -order_by => set the order by sort method

See Bio::Node::Node::each_Descendent()

⭐ next_tree

  • Title : next_tree
  • Usage : my $tree = $treeio->next_tree
  • Function : Gets the next tree in the stream
  • Returns : Bio::Tree::TreeI
  • Args : none

⭐ write_tree

  • Title : write_tree
  • Usage : $treeio->write_tree($tree);
  • Function : Write a tree out to data stream in newick/phylip format
  • Returns : none
  • Args : Bio::Tree::TreeI object
  • Title : print_tree_count
  • Usage : $obj->print_tree_count($newval)
  • Function : Get/Set flag for printing out the tree count (paml, protml way)
  • Returns : value of print_tree_count (a scalar)
  • Args : on set, new value (a scalar or undef, optional)

⭐ bootstrap_style

  • Title : bootstrap_style
  • Usage : $obj->bootstrap_style($newval)
  • Function : A description of how bootstraps and branch lengths are written, as the ID part of the internal node or else in [] in the branch length (Molphy-like; I am sure there is a better name for this but am not sure where to go for some sort of format documentation)

If no branch lengths are requested then no bootstraps are usually written (unless someone REALLY wants this functionality…)

Can take on strings which contain the possible values of:

  • 'nobranchlength' —> don't draw any branch lengths — this is helpful if you don't want to have to go through and delete branch len on all nodes
  • 'molphy' —> draw bootstraps (100) like (A:0.11,B:0.22):0.33[100];
  • 'traditional' —> draw bootstraps (100) like (A:0.11,B:0.22)100:0.33;
  • Returns : value of bootstrap_style (a scalar)
  • Args : on set, new value (a scalar or undef, optional)

⭐ order_by

  • Title : order_by
  • Usage : $obj->order_by($newval)
  • Function : Allow node order to be specified (typically "alpha")

See Bio::Node::Node::each_Descendent()

  • Returns : value of order_by (a scalar)
  • Args : on set, new value (a scalar or undef, optional)

and that's the whole page, bestie!! 🎀✨ this lil masterpiece is running on perl v5.32.1, dated 2021-08-15, and it's part of the User Contributed Perl Documentation for Bio::TreeIO::newick (3pm). mwah. go parse a tree. 💅🌳💖

📦 where this page comes from