Routines for manipulating Newick Format phylogenetic trees in Ruby
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newick-ruby.gemspec

README

Ruby routines for manipulating Newick trees. See http://en.wikipedia.org/wiki/Newick_format for a description of what Newick trees are if you don't know, but chances are, if you don't already know, this isn't going to be very useful code to you.

I'm aware that BioRuby has Newick routines as of late, although I'm not sure if they do all my code does, plus I started my code several years ago when BioRuby was just starting out. I'm all for anyone taking what they find useful from my code and integrating it into BioRuby, though.

One of things I'm most proud of is my midpoint rooting method, as I have yet to see another command-line rerooting method that can take in arbitrary Newick trees. 

I've created wrappers around most of the major functionality of my code, such as rerooting and drawing trees. The tree drawing routines (and its wrapper newickDraw) use the fpdf gem for rendering PDF files. Other than that, my code is stand alone.

jgi_19094_1366.m000227-Phatr2.tree is an example Newick tree for playing with the routines.

Let me know what you think:

Jonathan Badger
National Cancer Institute (NCI)
jhbadger@gmail.com

UPDATES:
1.0.2 -- faster distance matrix calculation
1.0.3 -- fixed colors in highlights when drawing trees
1.0.4 -- allow choice of exact or inexact node matching

License
(The MIT License)

Copyright © 2010 Jonathan Badger

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the ‘Software’), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED ‘AS IS’, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.