bio-raxml 0.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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+ lib/**/*.rb
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+ bin/*
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+ -
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+ features/**/*.feature
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+ LICENSE.txt
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+ language: ruby
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+ rvm:
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+ - 1.9.2
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+ - 1.9.3
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+ - jruby-19mode # JRuby in 1.9 mode
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+ - rbx-19mode
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+ # - 1.8.7
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+ # - jruby-18mode # JRuby in 1.8 mode
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+ # - rbx-18mode
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+
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+ # uncomment this line if your project needs to run something other than `rake`:
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+ # script: bundle exec rspec spec
data/Gemfile ADDED
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+ source "http://rubygems.org"
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+ # Add dependencies required to use your gem here.
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+ # Example:
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+ # gem "activesupport", ">= 2.3.5"
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+
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+ # Add dependencies to develop your gem here.
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+ # Include everything needed to run rake, tests, features, etc.
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+ group :development do
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+ gem "shoulda", ">= 0"
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+ gem "rdoc", "~> 3.12"
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+ gem "bundler", "~> 1.3.5"
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+ gem "jeweler", "~> 1.8.4"
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+ gem "bio", ">= 1.4.2"
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+ gem "rdoc", "~> 3.12"
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+ end
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+ Copyright (c) 2013 Fernando Izquierdo
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ "Software"), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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+ # bio-raxml
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+
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+ [![Build Status](https://secure.travis-ci.org/fizquierdo/bioruby-raxml.png)](http://travis-ci.org/fizquierdo/bioruby-raxml)
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+
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+ Full description goes here
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+
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+ Note: this software is under active development!
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+
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+ ## Installation
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+
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+ ```sh
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+ gem install bio-raxml
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+ ```
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+
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+ ## Usage
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+
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+ ```ruby
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+ require 'bio-raxml'
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+ ```
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+
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+ The API doc is online. For more code examples see the test files in
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+ the source tree.
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+
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+ ## Project home page
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+
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+ Information on the source tree, documentation, examples, issues and
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+ how to contribute, see
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+
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+ http://github.com/fizquierdo/bioruby-raxml
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+
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+ The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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+
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+ ## Cite
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+
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+ If you use this software, please cite one of
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+
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+ * [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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+ * [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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+
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+ ## Biogems.info
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+
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+ This Biogem is published at [#bio-raxml](http://biogems.info/index.html)
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+
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+ ## Copyright
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+
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+ Copyright (c) 2013 Fernando Izquierdo. See LICENSE.txt for further details.
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+
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+ = bio-raxml
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+
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+ {<img
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+ src="https://secure.travis-ci.org/fizquierdo/bioruby-raxml.png"
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+ />}[http://travis-ci.org/#!/fizquierdo/bioruby-raxml]
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+
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+ Full description goes here
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+
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+ Note: this software is under active development!
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+
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+ == Installation
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+
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+ gem install bio-raxml
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+
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+ == Usage
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+
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+ == Developers
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+
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+ To use the library
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+
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+ require 'bio-raxml'
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+
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+ The API doc is online. For more code examples see also the test files in
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+ the source tree.
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+
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+ == Project home page
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+
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+ Information on the source tree, documentation, issues and how to contribute, see
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+
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+ http://github.com/fizquierdo/bioruby-raxml
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+
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+ The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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+
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+ == Cite
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+
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+ If you use this software, please cite one of
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+
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+ * [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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+ * [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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+
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+ == Biogems.info
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+
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+ This Biogem is published at http://biogems.info/index.html#bio-raxml
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+
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+ == Copyright
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+
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+ Copyright (c) 2013 Fernando Izquierdo. See LICENSE.txt for further details.
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+
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+ # encoding: utf-8
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+
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+ require 'rubygems'
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+ require 'bundler'
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+ begin
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+ Bundler.setup(:default, :development)
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+ rescue Bundler::BundlerError => e
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+ $stderr.puts e.message
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+ $stderr.puts "Run `bundle install` to install missing gems"
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+ exit e.status_code
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+ end
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+ require 'rake'
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+
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+ require 'jeweler'
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+ Jeweler::Tasks.new do |gem|
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+ # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
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+ gem.name = "bio-raxml"
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+ gem.homepage = "http://github.com/fizquierdo/bioruby-raxml"
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+ gem.license = "MIT"
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+ gem.summary = %Q{Ruby wrapper to run standard-RAxML for Maximum Likelihood tree inference}
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+ gem.description = %Q{Just a test}
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+ gem.email = "fer.izquierdo@gmail.com"
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+ gem.authors = ["Fernando Izquierdo"]
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+ # dependencies defined in Gemfile
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+ end
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+ Jeweler::RubygemsDotOrgTasks.new
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+
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+ require 'rake/testtask'
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+ Rake::TestTask.new(:test) do |test|
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+ test.libs << 'lib' << 'test'
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+ test.pattern = 'test/**/test_*.rb'
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+ test.verbose = true
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+ end
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+
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+ task :default => :test
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+
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+ require 'rdoc/task'
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+ Rake::RDocTask.new do |rdoc|
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+ version = File.exist?('VERSION') ? File.read('VERSION') : ""
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+
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+ rdoc.rdoc_dir = 'rdoc'
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+ rdoc.title = "bio-raxml #{version}"
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+ rdoc.rdoc_files.include('README*')
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+ rdoc.rdoc_files.include('lib/**/*.rb')
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+ end
data/VERSION ADDED
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+ 0.1.0
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+ #!/usr/bin/env ruby
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+ #
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+
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+ load "../lib/bio-raxml/raxml.rb"
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+
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+ input = {phylip: "../testdata/lonicera_10taxa.rbcL.phy", name: "test"}
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+
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+ puts "Test with #{input.to_s}"
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+ raxml = BioRaxml::Raxml.new input
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+
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+ puts raxml.run_cmd
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+
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+ system raxml.run_cmd
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+ # Please require your code below, respecting the naming conventions in the
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+ # bioruby directory tree.
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+ #
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+ # For example, say you have a plugin named bio-plugin, the only uncommented
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+ # line in this file would be
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+ #
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+ # require 'bio/bio-plugin/plugin'
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+ #
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+ # In this file only require other files. Avoid other source code.
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+
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+ require 'bio-raxml/raxml.rb'
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+
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+ module BioRaxml
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+ class Raxml
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+ def initialize(opts)
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+ @phylip = opts[:phylip]
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+ @name = opts[:name]
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+ end
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+ def run_cmd
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+ cmd = "raxmlHPC-SSE3 -s #{@phylip} -n #{@name} -p 12345 -m GTRGAMMA"
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+ end
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+ end
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+ end
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+ require 'rubygems'
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+ require 'bundler'
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+ begin
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+ Bundler.setup(:default, :development)
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+ rescue Bundler::BundlerError => e
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+ $stderr.puts e.message
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+ $stderr.puts "Run `bundle install` to install missing gems"
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+ exit e.status_code
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+ end
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+ require 'test/unit'
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+ require 'shoulda'
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+
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+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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+ $LOAD_PATH.unshift(File.dirname(__FILE__))
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+ require 'bio-raxml'
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+
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+ class Test::Unit::TestCase
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+ end
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+ require 'helper'
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+
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+ class TestBioRaxml < Test::Unit::TestCase
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+ should "probably rename this file and start testing for real" do
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+ flunk "hey buddy, you should probably rename this file and start testing for real"
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+ end
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+ end
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+ 10 1428
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+ Lonicera_nervosa atgtcaccacaaacagagactaaagcaagtgttggattcaaagctggtgttaaagagtacaaattgacttattatactcctgagtaccaaaccaaggatactgatatattggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggctgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggngatgctaccacatcgagcccgttgctggagaagaaactcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttggnttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtcgcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggtcgtcccctgttnnnatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccatttttaaagcacaaactgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagacatgatgaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccaccttggctcactattgccgagataatggcctacttcttcacatccaccgcgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagcgttacgtatgtctggtggagatcatattcacgccggtaccgtagtaggtaaacttgaaggggaaagagaaatcactttgggctttgttgatttactgcgtgatgattttattgaaaaggatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgccngctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggnnaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtaaaagctcgtaatgaaggacgtgatcttgctcaggaaggtaatgaaattattcgcgaggcttgcaaatggagcccggaactagctgctgcttgtgaagtatggaaagagatcgtatttaattttgcagcagtggacgttttgtaa
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+ Lonicera_reticulata --------------------------aagtgttggattcaaagctggtgttaaagagtacaaattgacttattatactcctgagtaccaaaccaaggatactgatatattggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggctgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggngatgctaccacatcgagcccgttgctggagaagaaactcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttggnttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtcgcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggtcgtcccctgttnnnatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccatttttaaagcacaaactgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagacatgatgaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccaccttggctcactattgccgagataatggcctacttcttcacatccaccgcgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagcgttacgtatgtctggtggagatcatattcacgccggtaccgtagtaggtaaacttgaaggggaaagagaaatcactttgggctttgttgatttactgcgtgatgattttattgaaaaggatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgccngctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggnnaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtaaaagctcgtaatgaaggacgtgatcttgctcaggaaggtaatgaaattattcgcgaggcttgcaaatggagcccggaactagctgctgcttgtgaagtatggaaagagatcgtatttaattttgcagcagtggacgttttggat
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+ Lonicera_albiflora ---------------------------------------------------------------ttgacttattatactcctgactatgaaaccaaagatactgatatcttggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggccgcggtagatgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaaggtcgatgctaccacatcgagcccgttgctggagaagaaactcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtcgcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccttgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcagtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttataaagcacaagctgaaacaggtgaaatcaaagggcattacttgatg---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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+ Lonicera_periclymenum --------------------------aagtgttggattcaaagcgggtgttaaagattacaaattgacttattatactcctgactatgaaaccaaagatactgatatcttggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggttt--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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+ Lonicera_japonica -----------------------------------------------------------------------------------------------------------------------------------------------------------agcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttttaaagcacaagttgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagaaatgatcaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccagcctggctcactattgccgagataatggcctacttcttcacatccaccgtgcaatgcatgcagttattgatagacagaagaatcatggtatacactttcgtgtactagctaaagcgttacgtatgtctggtggagatcatattcactccggtaccgtagtaggtaaacttgaaggggaaagagagatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcg----------------------------------------------------------------------------------------------------------------------------------------
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+ Lonicera_fulvotomentosa -----------------------------------------------------------------------------------------------------------------------------------------------------------agcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaggggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttttaaagcacaagttgaaacaggtgaaatcaaaggtcattacttgaatgctactgcaggtacatgtgaagaaatgatgaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccaccctggctcactattgccgagataatggcctacttcttcacatccaccgtgcaatgcatgcagttattgatagacagaagaatcatggtatacactttcgtgtactagctaaagcgttacgtatgtctggtggagatcatattcacgccggtaccgtagtaggtaaacttgaaggggaaagagagatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcg----------------------------------------------------------------------------------------------------------------------------------------
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+ Lonicera_macranthoides -----------------------------------------------------------------------------------------------------------------------------------------------------------agcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttttaaagcacaagttgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagaaatgatgaaaagggctgtatttgccagagaattgggagctcctatcataatgcacgactacttaacagggggattcactgcaaataccaccctggctcactattgccgagataatggcctacttcttcacatccaccgtgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagggttacgtatgtctggtggagatcatattcatgccggtaccgtagtaggtaaacttgaaggggaaagagagatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcatgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcg----------------------------------------------------------------------------------------------------------------------------------------
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+ Lonicera_confusa -----------------------------------------------------------------------------------------------------------------------------------------------------------agcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttttaaagcacaagttgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagaaatgatgaaaagggctgtatttgccagagaattgggagctcctatcataatgcacgactacttaacagggggattcactgcaaataccaccctggctcactattgccgagataatggcctacttcttcacatccaccgtgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagggttacgtatgtctggtggagatcatattcatgccggtaccgtagtaggtaaacttgaaggggaaagagagatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcg----------------------------------------------------------------------------------------------------------------------------------------
10
+ Lonicera_hypoglauca -----------------------------------------------------------------------------------------------------------------------------------------------------------agcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctaccacatcgagcccgttgctggagaagaaaatcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtctcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttttaaagcacaagttgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagaaatgatgaaaagggctgtatttgccagagaattgggagctcctatcataatgcacgactacttaacagggggattcactgcaaataccaccctggctcactattgccgagataatggcctacttcttcacatccaccgtgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagggttacgtatgtctggtggagatcatattcatgccggtaccgtagtaggtaaacttgaaggggaaagagagatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcatgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcg----------------------------------------------------------------------------------------------------------------------------------------
11
+ Lonicera_orientalis --------------------------aagtgttggattcaaagcgggtgttaaagattacaaattgacttattatactcctgaatatgaaaccaaagatactgatatcttggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggccgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggcgatgctacggcatcgagcccgttgctggagaagaaaatcaatatattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttgggttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgctgcttatgttaaaactttccaaggcccgcctcatgggattcaagttgagagagataaattgaacaagtacggccgccccctgttgggatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccctttataaagcacaaactgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagaaatgatcaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccaccttggctcactattgccgagataatggcctacttctttacatccaccgcgcaatgcatgcagttattgatagacagaagaatcatggtatccatttccgcgtactagcaaaagcgttacgtatgtctggtggagatcatattcacgccggtaccgtagtaggtaaacttgaaggggaaagagaaatcactttgggctttgttgatttactgcgcgatgattttattgaaaaagatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgcccgctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggggaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtacaagctcgtaatgaggggcgtgatcttgctcgtgacggtaatgaaattatccgtgcggcttgcaaatggagtcctgaactagctgctgcttgtgaggtatggaaggagatcaaatttgaatttgaagctatggatactttgtaa
@@ -0,0 +1,10 @@
1
+ 9 1428
2
+ Lonicera_nervosa ATGTCACCACAAACAGAGACTAAAGCAAGTGTTGGATTCAAAGCTGGTGTTAAAGAGTACAAATTGACTTATTATACTCCTGAGTACCAAACCAAGGATACTGATATATTGGCAGCATTCCGAGTAACTCCTCAACCCGGAGTTCCGCCTGAAGAAGCGGGGGCTGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGG-GATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAACTCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGG-TTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCGCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGTCGTCCCCTGTT---ATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCATTTTTAAAGCACAAACTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGACATGATGAAAAGGGCTGTATTTGCCAGAGAATTGGGAGTTCCTATCGTAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCTTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGCGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATGCACTTTCGTGTACTAGCTAAAGCGTTACGTATGTCTGGTGGAGATCATATTCACGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAAATCACTTTGGGCTTTGTTGATTTACTGCGTGATGATTTTATTGAAAAGGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCC-GCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGG--AAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTAAAAGCTCGTAATGAAGGACGTGATCTTGCTCAGGAAGGTAATGAAATTATTCGCGAGGCTTGCAAATGGAGCCCGGAACTAGCTGCTGCTTGTGAAGTATGGAAAGAGATCGTATTTAATTTTGCAGCAGTGGACGTTTTGTAA
3
+ Lonicera_reticulata --------------------------AAGTGTTGGATTCAAAGCTGGTGTTAAAGAGTACAAATTGACTTATTATACTCCTGAGTACCAAACCAAGGATACTGATATATTGGCAGCATTCCGAGTAACTCCTCAACCCGGAGTTCCGCCTGAAGAAGCGGGGGCTGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGG-GATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAACTCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGG-TTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCGCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGTCGTCCCCTGTT---ATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCATTTTTAAAGCACAAACTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGACATGATGAAAAGGGCTGTATTTGCCAGAGAATTGGGAGTTCCTATCGTAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCTTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGCGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATGCACTTTCGTGTACTAGCTAAAGCGTTACGTATGTCTGGTGGAGATCATATTCACGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAAATCACTTTGGGCTTTGTTGATTTACTGCGTGATGATTTTATTGAAAAGGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCC-GCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGG--AAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTAAAAGCTCGTAATGAAGGACGTGATCTTGCTCAGGAAGGTAATGAAATTATTCGCGAGGCTTGCAAATGGAGCCCGGAACTAGCTGCTGCTTGTGAAGTATGGAAAGAGATCGTATTTAATTTTGCAGCAGTGGACGTTTTGGAT
4
+ Lonicera_albiflora ---------------------------------------------------------------TTGACTTATTATACTCCTGACTATGAAACCAAAGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCCGGAGTTCCGCCTGAAGAAGCGGGGGCCGCGGTAGATGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGTCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAACTCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCGCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCTTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCAGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTATAAAGCACAAGCTGAAACAGGTGAAATCAAAGGGCATTACTTGATG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
5
+ Lonicera_periclymenum --------------------------AAGTGTTGGATTCAAAGCGGGTGTTAAAGATTACAAATTGACTTATTATACTCCTGACTATGAAACCAAAGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCCGGAGTTCCGCCTGAAGAAGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGGCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAAATCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCTCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
6
+ Lonicera_japonica -----------------------------------------------------------------------------------------------------------------------------------------------------------AGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGGCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAAATCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCTCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTTTAAAGCACAAGTTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGAAATGATCAAAAGGGCTGTATTTGCCAGAGAATTGGGAGTTCCTATCGTAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCAGCCTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGTGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATACACTTTCGTGTACTAGCTAAAGCGTTACGTATGTCTGGTGGAGATCATATTCACTCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAGATCACTTTGGGCTTTGTTGATTTACTGCGCGATGATTTTATTGAAAAAGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCCCGCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGGGGAAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTACAAGCTCG----------------------------------------------------------------------------------------------------------------------------------------
7
+ Lonicera_fulvotomentosa -----------------------------------------------------------------------------------------------------------------------------------------------------------AGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAGGGGCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAAATCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCTCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTTTAAAGCACAAGTTGAAACAGGTGAAATCAAAGGTCATTACTTGAATGCTACTGCAGGTACATGTGAAGAAATGATGAAAAGGGCTGTATTTGCCAGAGAATTGGGAGTTCCTATCGTAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCCTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGTGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATACACTTTCGTGTACTAGCTAAAGCGTTACGTATGTCTGGTGGAGATCATATTCACGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAGATCACTTTGGGCTTTGTTGATTTACTGCGCGATGATTTTATTGAAAAAGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCCCGCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGGGGAAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTACAAGCTCG----------------------------------------------------------------------------------------------------------------------------------------
8
+ Lonicera_macranthoides -----------------------------------------------------------------------------------------------------------------------------------------------------------AGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGGCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAAATCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCTCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTTTAAAGCACAAGTTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGAAATGATGAAAAGGGCTGTATTTGCCAGAGAATTGGGAGCTCCTATCATAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCCTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGTGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATGCACTTTCGTGTACTAGCTAAAGGGTTACGTATGTCTGGTGGAGATCATATTCATGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAGATCACTTTGGGCTTTGTTGATTTACTGCGCGATGATTTTATTGAAAAAGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCATGTTTGGCATATGCCCGCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGGGGAAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTACAAGCTCG----------------------------------------------------------------------------------------------------------------------------------------
9
+ Lonicera_confusa -----------------------------------------------------------------------------------------------------------------------------------------------------------AGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGGCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAAATCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGTCTCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTTTAAAGCACAAGTTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGAAATGATGAAAAGGGCTGTATTTGCCAGAGAATTGGGAGCTCCTATCATAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCCTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTCACATCCACCGTGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATGCACTTTCGTGTACTAGCTAAAGGGTTACGTATGTCTGGTGGAGATCATATTCATGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAGATCACTTTGGGCTTTGTTGATTTACTGCGCGATGATTTTATTGAAAAAGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCCCGCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGGGGAAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTACAAGCTCG----------------------------------------------------------------------------------------------------------------------------------------
10
+ Lonicera_orientalis --------------------------AAGTGTTGGATTCAAAGCGGGTGTTAAAGATTACAAATTGACTTATTATACTCCTGAATATGAAACCAAAGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCCGGAGTTCCGCCTGAAGAAGCGGGGGCCGCGGTAGCTGCTGAATCTTCAACCGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGGCGATGCTACGGCATCGAGCCCGTTGCTGGAGAAGAAAATCAATATATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCTATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATCCCTGCTGCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGGATTCAAGTTGAGAGAGATAAATTGAACAAGTACGGCCGCCCCCTGTTGGGATGTACTATTAAACCTAAATTGGGGTTATCTGCTAAAAACTACGGTAGGGCGGTTTATGAATGTCTACGTGGTGGACTTGATTTTACCAAAGATGATGAGAACGTGAACTCCCAACCATTTATGCGTTGGAGAGATCGTTTCTTATTTTGTGCCGAAGCCCTTTATAAAGCACAAACTGAAACAGGTGAAATCAAAGGGCATTACTTGAATGCTACTGCAGGTACATGTGAAGAAATGATCAAAAGGGCTGTATTTGCCAGAGAATTGGGAGTTCCTATCGTAATGCACGACTACTTAACAGGGGGATTCACTGCAAATACCACCTTGGCTCACTATTGCCGAGATAATGGCCTACTTCTTTACATCCACCGCGCAATGCATGCAGTTATTGATAGACAGAAGAATCATGGTATCCATTTCCGCGTACTAGCAAAAGCGTTACGTATGTCTGGTGGAGATCATATTCACGCCGGTACCGTAGTAGGTAAACTTGAAGGGGAAAGAGAAATCACTTTGGGCTTTGTTGATTTACTGCGCGATGATTTTATTGAAAAAGATCGAAGTCGCGGTATTTATTTCACTCAAGATTGGGTCTCTCTACCGGGTGTTCTGCCCGTGGCTTCGGGGGGTATTCACGTTTGGCATATGCCCGCTTTGACCGAGATCTTTGGAGATGATTCCGTCCTACAGTTCGGCGGAGGAACTTTAGGACACCCTTGGGGAAATGCACCTGGTGCCGTAGCTAATCGAGTCGCTCTAGAAGCATGTGTACAAGCTCGTAATGAGGGGCGTGATCTTGCTCGTGACGGTAATGAAATTATCCGTGCGGCTTGCAAATGGAGTCCTGAACTAGCTGCTGCTTGTGAGGTATGGAAGGAGATCAAATTTGAATTTGAAGCTATGGATACTTTGTAA
metadata ADDED
@@ -0,0 +1,132 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: bio-raxml
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.1.0
5
+ prerelease:
6
+ platform: ruby
7
+ authors:
8
+ - Fernando Izquierdo
9
+ autorequire:
10
+ bindir: bin
11
+ cert_chain: []
12
+ date: 2013-07-16 00:00:00.000000000 Z
13
+ dependencies:
14
+ - !ruby/object:Gem::Dependency
15
+ name: shoulda
16
+ requirement: &12320140 !ruby/object:Gem::Requirement
17
+ none: false
18
+ requirements:
19
+ - - ! '>='
20
+ - !ruby/object:Gem::Version
21
+ version: '0'
22
+ type: :development
23
+ prerelease: false
24
+ version_requirements: *12320140
25
+ - !ruby/object:Gem::Dependency
26
+ name: rdoc
27
+ requirement: &12736220 !ruby/object:Gem::Requirement
28
+ none: false
29
+ requirements:
30
+ - - ~>
31
+ - !ruby/object:Gem::Version
32
+ version: '3.12'
33
+ type: :development
34
+ prerelease: false
35
+ version_requirements: *12736220
36
+ - !ruby/object:Gem::Dependency
37
+ name: bundler
38
+ requirement: &12735520 !ruby/object:Gem::Requirement
39
+ none: false
40
+ requirements:
41
+ - - ~>
42
+ - !ruby/object:Gem::Version
43
+ version: 1.3.5
44
+ type: :development
45
+ prerelease: false
46
+ version_requirements: *12735520
47
+ - !ruby/object:Gem::Dependency
48
+ name: jeweler
49
+ requirement: &12734720 !ruby/object:Gem::Requirement
50
+ none: false
51
+ requirements:
52
+ - - ~>
53
+ - !ruby/object:Gem::Version
54
+ version: 1.8.4
55
+ type: :development
56
+ prerelease: false
57
+ version_requirements: *12734720
58
+ - !ruby/object:Gem::Dependency
59
+ name: bio
60
+ requirement: &12733800 !ruby/object:Gem::Requirement
61
+ none: false
62
+ requirements:
63
+ - - ! '>='
64
+ - !ruby/object:Gem::Version
65
+ version: 1.4.2
66
+ type: :development
67
+ prerelease: false
68
+ version_requirements: *12733800
69
+ - !ruby/object:Gem::Dependency
70
+ name: rdoc
71
+ requirement: &12732080 !ruby/object:Gem::Requirement
72
+ none: false
73
+ requirements:
74
+ - - ~>
75
+ - !ruby/object:Gem::Version
76
+ version: '3.12'
77
+ type: :development
78
+ prerelease: false
79
+ version_requirements: *12732080
80
+ description: Just a test
81
+ email: fer.izquierdo@gmail.com
82
+ executables: []
83
+ extensions: []
84
+ extra_rdoc_files:
85
+ - LICENSE.txt
86
+ - README.md
87
+ - README.rdoc
88
+ files:
89
+ - .document
90
+ - .travis.yml
91
+ - Gemfile
92
+ - LICENSE.txt
93
+ - README.md
94
+ - README.rdoc
95
+ - Rakefile
96
+ - VERSION
97
+ - example/run_raxml.rb
98
+ - lib/bio-raxml.rb
99
+ - lib/bio-raxml/raxml.rb
100
+ - test/helper.rb
101
+ - test/test_bio-raxml.rb
102
+ - testdata/lonicera_10taxa.rbcL.phy
103
+ - testdata/lonicera_10taxa.rbcL.phy.reduced
104
+ homepage: http://github.com/fizquierdo/bioruby-raxml
105
+ licenses:
106
+ - MIT
107
+ post_install_message:
108
+ rdoc_options: []
109
+ require_paths:
110
+ - lib
111
+ required_ruby_version: !ruby/object:Gem::Requirement
112
+ none: false
113
+ requirements:
114
+ - - ! '>='
115
+ - !ruby/object:Gem::Version
116
+ version: '0'
117
+ segments:
118
+ - 0
119
+ hash: 3073763365429768198
120
+ required_rubygems_version: !ruby/object:Gem::Requirement
121
+ none: false
122
+ requirements:
123
+ - - ! '>='
124
+ - !ruby/object:Gem::Version
125
+ version: '0'
126
+ requirements: []
127
+ rubyforge_project:
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+ rubygems_version: 1.8.10
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+ signing_key:
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+ specification_version: 3
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+ summary: Ruby wrapper to run standard-RAxML for Maximum Likelihood tree inference
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+ test_files: []