bio-raxml 0.1.0

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

@@ -0,0 +1,15 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "~> 1.3.5"
+  gem "jeweler", "~> 1.8.4"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2013 Fernando Izquierdo
+
+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.

data/README.md

@@ -0,0 +1,47 @@
+# bio-raxml
+
+[![Build Status](https://secure.travis-ci.org/fizquierdo/bioruby-raxml.png)](http://travis-ci.org/fizquierdo/bioruby-raxml)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install bio-raxml
+```
+
+## Usage
+
+```ruby
+    require 'bio-raxml'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/fizquierdo/bioruby-raxml
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at [#bio-raxml](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2013 Fernando Izquierdo. See LICENSE.txt for further details.
+

data/README.rdoc

@@ -0,0 +1,48 @@
+= bio-raxml
+
+{<img
+src="https://secure.travis-ci.org/fizquierdo/bioruby-raxml.png"
+/>}[http://travis-ci.org/#!/fizquierdo/bioruby-raxml]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-raxml
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-raxml'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/fizquierdo/bioruby-raxml
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-raxml
+
+== Copyright
+
+Copyright (c) 2013 Fernando Izquierdo. See LICENSE.txt for further details.
+

data/Rakefile

@@ -0,0 +1,45 @@
+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-raxml"
+  gem.homepage = "http://github.com/fizquierdo/bioruby-raxml"
+  gem.license = "MIT"
+  gem.summary = %Q{Ruby wrapper to run standard-RAxML for Maximum Likelihood tree inference}
+  gem.description = %Q{Just a test}
+  gem.email = "fer.izquierdo@gmail.com"
+  gem.authors = ["Fernando Izquierdo"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-raxml #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

@@ -0,0 +1 @@
+0.1.0

data/example/run_raxml.rb

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+#!/usr/bin/env ruby
+#
+
+load "../lib/bio-raxml/raxml.rb"
+
+input = {phylip: "../testdata/lonicera_10taxa.rbcL.phy", name: "test"}
+
+puts "Test with #{input.to_s}"
+raxml = BioRaxml::Raxml.new input
+
+puts raxml.run_cmd
+
+system raxml.run_cmd

data/lib/bio-raxml.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-raxml/raxml.rb'
+

data/lib/bio-raxml/raxml.rb

@@ -0,0 +1,11 @@
+module BioRaxml
+  class Raxml
+    def initialize(opts)
+      @phylip = opts[:phylip]
+      @name = opts[:name]
+    end
+    def run_cmd
+      cmd = "raxmlHPC-SSE3 -s #{@phylip} -n #{@name} -p 12345 -m GTRGAMMA"
+    end
+  end
+end

data/test/helper.rb

@@ -0,0 +1,18 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-raxml'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-raxml.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestBioRaxml < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

data/testdata/lonicera_10taxa.rbcL.phy

@@ -0,0 +1,11 @@
+10 1428
+Lonicera_nervosa atgtcaccacaaacagagactaaagcaagtgttggattcaaagctggtgttaaagagtacaaattgacttattatactcctgagtaccaaaccaaggatactgatatattggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggctgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggngatgctaccacatcgagcccgttgctggagaagaaactcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttggnttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtcgcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggtcgtcccctgttnnnatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccatttttaaagcacaaactgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagacatgatgaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccaccttggctcactattgccgagataatggcctacttcttcacatccaccgcgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagcgttacgtatgtctggtggagatcatattcacgccggtaccgtagtaggtaaacttgaaggggaaagagaaatcactttgggctttgttgatttactgcgtgatgattttattgaaaaggatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgccngctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggnnaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtaaaagctcgtaatgaaggacgtgatcttgctcaggaaggtaatgaaattattcgcgaggcttgcaaatggagcccggaactagctgctgcttgtgaagtatggaaagagatcgtatttaattttgcagcagtggacgttttgtaa
+Lonicera_reticulata --------------------------aagtgttggattcaaagctggtgttaaagagtacaaattgacttattatactcctgagtaccaaaccaaggatactgatatattggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggctgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggngatgctaccacatcgagcccgttgctggagaagaaactcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttggnttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtcgcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggtcgtcccctgttnnnatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccatttttaaagcacaaactgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagacatgatgaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccaccttggctcactattgccgagataatggcctacttcttcacatccaccgcgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagcgttacgtatgtctggtggagatcatattcacgccggtaccgtagtaggtaaacttgaaggggaaagagaaatcactttgggctttgttgatttactgcgtgatgattttattgaaaaggatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgccngctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggnnaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtaaaagctcgtaatgaaggacgtgatcttgctcaggaaggtaatgaaattattcgcgaggcttgcaaatggagcccggaactagctgctgcttgtgaagtatggaaagagatcgtatttaattttgcagcagtggacgttttggat
+Lonicera_albiflora ---------------------------------------------------------------ttgacttattatactcctgactatgaaaccaaagatactgatatcttggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggccgcggtagatgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaaggtcgatgctaccacatcgagcccgttgctggagaagaaactcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtcgcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccttgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcagtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttataaagcacaagctgaaacaggtgaaatcaaagggcattacttgatg---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_periclymenum --------------------------aagtgttggattcaaagcgggtgttaaagattacaaattgacttattatactcctgactatgaaaccaaagatactgatatcttggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggttt--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_japonica -----------------------------------------------------------------------------------------------------------------------------------------------------------agcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttttaaagcacaagttgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagaaatgatcaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccagcctggctcactattgccgagataatggcctacttcttcacatccaccgtgcaatgcatgcagttattgatagacagaagaatcatggtatacactttcgtgtactagctaaagcgttacgtatgtctggtggagatcatattcactccggtaccgtagtaggtaaacttgaaggggaaagagagatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcg----------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_fulvotomentosa -----------------------------------------------------------------------------------------------------------------------------------------------------------agcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaggggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttttaaagcacaagttgaaacaggtgaaatcaaaggtcattacttgaatgctactgcaggtacatgtgaagaaatgatgaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccaccctggctcactattgccgagataatggcctacttcttcacatccaccgtgcaatgcatgcagttattgatagacagaagaatcatggtatacactttcgtgtactagctaaagcgttacgtatgtctggtggagatcatattcacgccggtaccgtagtaggtaaacttgaaggggaaagagagatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcg----------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_macranthoides -----------------------------------------------------------------------------------------------------------------------------------------------------------agcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttttaaagcacaagttgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagaaatgatgaaaagggctgtatttgccagagaattgggagctcctatcataatgcacgactacttaacagggggattcactgcaaataccaccctggctcactattgccgagataatggcctacttcttcacatccaccgtgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagggttacgtatgtctggtggagatcatattcatgccggtaccgtagtaggtaaacttgaaggggaaagagagatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcatgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcg----------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_confusa -----------------------------------------------------------------------------------------------------------------------------------------------------------agcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttttaaagcacaagttgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagaaatgatgaaaagggctgtatttgccagagaattgggagctcctatcataatgcacgactacttaacagggggattcactgcaaataccaccctggctcactattgccgagataatggcctacttcttcacatccaccgtgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagggttacgtatgtctggtggagatcatattcatgccggtaccgtagtaggtaaacttgaaggggaaagagagatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcg----------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_hypoglauca -----------------------------------------------------------------------------------------------------------------------------------------------------------agcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttttaaagcacaagttgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagaaatgatgaaaagggctgtatttgccagagaattgggagctcctatcataatgcacgactacttaacagggggattcactgcaaataccaccctggctcactattgccgagataatggcctacttcttcacatccaccgtgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagggttacgtatgtctggtggagatcatattcatgccggtaccgtagtaggtaaacttgaaggggaaagagagatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcatgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcg----------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_orientalis --------------------------aagtgttggattcaaagcgggtgttaaagattacaaattgacttattatactcctgaatatgaaaccaaagatactgatatcttggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctacggcatcgagcccgttgctggagaagaaaatcaatatattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgctgcttatgttaaaactttccaaggcccgcctcatgggattcaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttataaagcacaaactgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagaaatgatcaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccaccttggctcactattgccgagataatggcctacttctttacatccaccgcgcaatgcatgcagttattgatagacagaagaatcatggtatccatttccgcgtactagcaaaagcgttacgtatgtctggtggagatcatattcacgccggtaccgtagtaggtaaacttgaaggggaaagagaaatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcgtaatgaggggcgtgatcttgctcgtgacggtaatgaaattatccgtgcggcttgcaaatggagtcctgaactagctgctgcttgtgaggtatggaaggagatcaaatttgaatttgaagctatggatactttgtaa

data/testdata/lonicera_10taxa.rbcL.phy.reduced

@@ -0,0 +1,10 @@
+9 1428
+Lonicera_nervosa ATGTCACCACAAACAGAGACTAAAGCAAGTGTTGGATTCAAAGCTGGTGTTAAAGAGTACAAATTGACTTATTATACTCCTGAGTACCAAACCAAGGATACTGATATATTGGCAGCATTCCGAGTAACTCCTCAACCCGGAGTTCCGCCTGAAGAAGCGGGGGCTGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGG-GATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAACTCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGG-TTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCGCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGTCGTCCCCTGTT---ATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCATTTTTAAAGCACAAACTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGACATGATGAAAAGGGCTGTATTTGCCAGAGAATTGGGAGTTCCTATCGTAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCTTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGCGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATGCACTTTCGTGTACTAGCTAAAGCGTTACGTATGTCTGGTGGAGATCATATTCACGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAAATCACTTTGGGCTTTGTTGATTTACTGCGTGATGATTTTATTGAAAAGGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCC-GCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGG--AAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTAAAAGCTCGTAATGAAGGACGTGATCTTGCTCAGGAAGGTAATGAAATTATTCGCGAGGCTTGCAAATGGAGCCCGGAACTAGCTGCTGCTTGTGAAGTATGGAAAGAGATCGTATTTAATTTTGCAGCAGTGGACGTTTTGTAA
+Lonicera_reticulata --------------------------AAGTGTTGGATTCAAAGCTGGTGTTAAAGAGTACAAATTGACTTATTATACTCCTGAGTACCAAACCAAGGATACTGATATATTGGCAGCATTCCGAGTAACTCCTCAACCCGGAGTTCCGCCTGAAGAAGCGGGGGCTGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGG-GATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAACTCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGG-TTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCGCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGTCGTCCCCTGTT---ATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCATTTTTAAAGCACAAACTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGACATGATGAAAAGGGCTGTATTTGCCAGAGAATTGGGAGTTCCTATCGTAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCTTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGCGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATGCACTTTCGTGTACTAGCTAAAGCGTTACGTATGTCTGGTGGAGATCATATTCACGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAAATCACTTTGGGCTTTGTTGATTTACTGCGTGATGATTTTATTGAAAAGGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCC-GCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGG--AAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTAAAAGCTCGTAATGAAGGACGTGATCTTGCTCAGGAAGGTAATGAAATTATTCGCGAGGCTTGCAAATGGAGCCCGGAACTAGCTGCTGCTTGTGAAGTATGGAAAGAGATCGTATTTAATTTTGCAGCAGTGGACGTTTTGGAT
+Lonicera_albiflora ---------------------------------------------------------------TTGACTTATTATACTCCTGACTATGAAACCAAAGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCCGGAGTTCCGCCTGAAGAAGCGGGGGCCGCGGTAGATGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGTCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAACTCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCGCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCTTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCAGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTATAAAGCACAAGCTGAAACAGGTGAAATCAAAGGGCATTACTTGATG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_periclymenum --------------------------AAGTGTTGGATTCAAAGCGGGTGTTAAAGATTACAAATTGACTTATTATACTCCTGACTATGAAACCAAAGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCCGGAGTTCCGCCTGAAGAAGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGGCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAAATCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCTCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_japonica -----------------------------------------------------------------------------------------------------------------------------------------------------------AGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGGCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAAATCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCTCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTTTAAAGCACAAGTTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGAAATGATCAAAAGGGCTGTATTTGCCAGAGAATTGGGAGTTCCTATCGTAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCAGCCTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGTGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATACACTTTCGTGTACTAGCTAAAGCGTTACGTATGTCTGGTGGAGATCATATTCACTCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAGATCACTTTGGGCTTTGTTGATTTACTGCGCGATGATTTTATTGAAAAAGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCCCGCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGGGGAAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTACAAGCTCG----------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_fulvotomentosa -----------------------------------------------------------------------------------------------------------------------------------------------------------AGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAGGGGCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAAATCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCTCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTTTAAAGCACAAGTTGAAACAGGTGAAATCAAAGGTCATTACTTGAATGCTACTGCAGGTACATGTGAAGAAATGATGAAAAGGGCTGTATTTGCCAGAGAATTGGGAGTTCCTATCGTAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCCTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGTGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATACACTTTCGTGTACTAGCTAAAGCGTTACGTATGTCTGGTGGAGATCATATTCACGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAGATCACTTTGGGCTTTGTTGATTTACTGCGCGATGATTTTATTGAAAAAGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCCCGCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGGGGAAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTACAAGCTCG----------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_macranthoides -----------------------------------------------------------------------------------------------------------------------------------------------------------AGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGGCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAAATCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCTCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTTTAAAGCACAAGTTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGAAATGATGAAAAGGGCTGTATTTGCCAGAGAATTGGGAGCTCCTATCATAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCCTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGTGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATGCACTTTCGTGTACTAGCTAAAGGGTTACGTATGTCTGGTGGAGATCATATTCATGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAGATCACTTTGGGCTTTGTTGATTTACTGCGCGATGATTTTATTGAAAAAGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCATGTTTGGCATATGCCCGCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGGGGAAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTACAAGCTCG----------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_confusa -----------------------------------------------------------------------------------------------------------------------------------------------------------AGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGGCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAAATCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCTCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTTTAAAGCACAAGTTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGAAATGATGAAAAGGGCTGTATTTGCCAGAGAATTGGGAGCTCCTATCATAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCCTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGTGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATGCACTTTCGTGTACTAGCTAAAGGGTTACGTATGTCTGGTGGAGATCATATTCATGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAGATCACTTTGGGCTTTGTTGATTTACTGCGCGATGATTTTATTGAAAAAGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCCCGCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGGGGAAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTACAAGCTCG----------------------------------------------------------------------------------------------------------------------------------------
+Lonicera_orientalis --------------------------AAGTGTTGGATTCAAAGCGGGTGTTAAAGATTACAAATTGACTTATTATACTCCTGAATATGAAACCAAAGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCCGGAGTTCCGCCTGAAGAAGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGGCGATGCTACGGCATCGAGCCCGTTGCTGGAGAAGAAAATCAATATATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGCTGCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGGATTCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTATAAAGCACAAACTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGAAATGATCAAAAGGGCTGTATTTGCCAGAGAATTGGGAGTTCCTATCGTAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCTTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTTACATCCACCGCGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATCCATTTCCGCGTACTAGCAAAAGCGTTACGTATGTCTGGTGGAGATCATATTCACGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAAATCACTTTGGGCTTTGTTGATTTACTGCGCGATGATTTTATTGAAAAAGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCCCGCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGGGGAAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTACAAGCTCGTAATGAGGGGCGTGATCTTGCTCGTGACGGTAATGAAATTATCCGTGCGGCTTGCAAATGGAGTCCTGAACTAGCTGCTGCTTGTGAGGTATGGAAGGAGATCAAATTTGAATTTGAAGCTATGGATACTTTGTAA

metadata

@@ -0,0 +1,132 @@
+--- !ruby/object:Gem::Specification
+name: bio-raxml
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- Fernando Izquierdo
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-07-16 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &12320140 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *12320140
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &12736220 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *12736220
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &12735520 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.5
+  type: :development
+  prerelease: false
+  version_requirements: *12735520
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &12734720 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: *12734720
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &12733800 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: *12733800
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &12732080 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *12732080
+description: Just a test
+email: fer.izquierdo@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- example/run_raxml.rb
+- lib/bio-raxml.rb
+- lib/bio-raxml/raxml.rb
+- test/helper.rb
+- test/test_bio-raxml.rb
+- testdata/lonicera_10taxa.rbcL.phy
+- testdata/lonicera_10taxa.rbcL.phy.reduced
+homepage: http://github.com/fizquierdo/bioruby-raxml
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 3073763365429768198
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.10
+signing_key: 
+specification_version: 3
+summary: Ruby wrapper to run standard-RAxML for Maximum Likelihood tree inference
+test_files: []