bio-raxml 0.1.0

Sign up to get free protection for your applications and to get access to all the features.
@@ -0,0 +1,5 @@
1
+ lib/**/*.rb
2
+ bin/*
3
+ -
4
+ features/**/*.feature
5
+ LICENSE.txt
@@ -0,0 +1,12 @@
1
+ language: ruby
2
+ rvm:
3
+ - 1.9.2
4
+ - 1.9.3
5
+ - jruby-19mode # JRuby in 1.9 mode
6
+ - rbx-19mode
7
+ # - 1.8.7
8
+ # - jruby-18mode # JRuby in 1.8 mode
9
+ # - rbx-18mode
10
+
11
+ # uncomment this line if your project needs to run something other than `rake`:
12
+ # script: bundle exec rspec spec
data/Gemfile ADDED
@@ -0,0 +1,15 @@
1
+ source "http://rubygems.org"
2
+ # Add dependencies required to use your gem here.
3
+ # Example:
4
+ # gem "activesupport", ">= 2.3.5"
5
+
6
+ # Add dependencies to develop your gem here.
7
+ # Include everything needed to run rake, tests, features, etc.
8
+ group :development do
9
+ gem "shoulda", ">= 0"
10
+ gem "rdoc", "~> 3.12"
11
+ gem "bundler", "~> 1.3.5"
12
+ gem "jeweler", "~> 1.8.4"
13
+ gem "bio", ">= 1.4.2"
14
+ gem "rdoc", "~> 3.12"
15
+ end
@@ -0,0 +1,20 @@
1
+ Copyright (c) 2013 Fernando Izquierdo
2
+
3
+ Permission is hereby granted, free of charge, to any person obtaining
4
+ a copy of this software and associated documentation files (the
5
+ "Software"), to deal in the Software without restriction, including
6
+ without limitation the rights to use, copy, modify, merge, publish,
7
+ distribute, sublicense, and/or sell copies of the Software, and to
8
+ permit persons to whom the Software is furnished to do so, subject to
9
+ the following conditions:
10
+
11
+ The above copyright notice and this permission notice shall be
12
+ included in all copies or substantial portions of the Software.
13
+
14
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
15
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
16
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
17
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
18
+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
19
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
20
+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
@@ -0,0 +1,47 @@
1
+ # bio-raxml
2
+
3
+ [![Build Status](https://secure.travis-ci.org/fizquierdo/bioruby-raxml.png)](http://travis-ci.org/fizquierdo/bioruby-raxml)
4
+
5
+ Full description goes here
6
+
7
+ Note: this software is under active development!
8
+
9
+ ## Installation
10
+
11
+ ```sh
12
+ gem install bio-raxml
13
+ ```
14
+
15
+ ## Usage
16
+
17
+ ```ruby
18
+ require 'bio-raxml'
19
+ ```
20
+
21
+ The API doc is online. For more code examples see the test files in
22
+ the source tree.
23
+
24
+ ## Project home page
25
+
26
+ Information on the source tree, documentation, examples, issues and
27
+ how to contribute, see
28
+
29
+ http://github.com/fizquierdo/bioruby-raxml
30
+
31
+ The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
32
+
33
+ ## Cite
34
+
35
+ If you use this software, please cite one of
36
+
37
+ * [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
38
+ * [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
39
+
40
+ ## Biogems.info
41
+
42
+ This Biogem is published at [#bio-raxml](http://biogems.info/index.html)
43
+
44
+ ## Copyright
45
+
46
+ Copyright (c) 2013 Fernando Izquierdo. See LICENSE.txt for further details.
47
+
@@ -0,0 +1,48 @@
1
+ = bio-raxml
2
+
3
+ {<img
4
+ src="https://secure.travis-ci.org/fizquierdo/bioruby-raxml.png"
5
+ />}[http://travis-ci.org/#!/fizquierdo/bioruby-raxml]
6
+
7
+ Full description goes here
8
+
9
+ Note: this software is under active development!
10
+
11
+ == Installation
12
+
13
+ gem install bio-raxml
14
+
15
+ == Usage
16
+
17
+ == Developers
18
+
19
+ To use the library
20
+
21
+ require 'bio-raxml'
22
+
23
+ The API doc is online. For more code examples see also the test files in
24
+ the source tree.
25
+
26
+ == Project home page
27
+
28
+ Information on the source tree, documentation, issues and how to contribute, see
29
+
30
+ http://github.com/fizquierdo/bioruby-raxml
31
+
32
+ The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
33
+
34
+ == Cite
35
+
36
+ If you use this software, please cite one of
37
+
38
+ * [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
39
+ * [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
40
+
41
+ == Biogems.info
42
+
43
+ This Biogem is published at http://biogems.info/index.html#bio-raxml
44
+
45
+ == Copyright
46
+
47
+ Copyright (c) 2013 Fernando Izquierdo. See LICENSE.txt for further details.
48
+
@@ -0,0 +1,45 @@
1
+ # encoding: utf-8
2
+
3
+ require 'rubygems'
4
+ require 'bundler'
5
+ begin
6
+ Bundler.setup(:default, :development)
7
+ rescue Bundler::BundlerError => e
8
+ $stderr.puts e.message
9
+ $stderr.puts "Run `bundle install` to install missing gems"
10
+ exit e.status_code
11
+ end
12
+ require 'rake'
13
+
14
+ require 'jeweler'
15
+ Jeweler::Tasks.new do |gem|
16
+ # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
17
+ gem.name = "bio-raxml"
18
+ gem.homepage = "http://github.com/fizquierdo/bioruby-raxml"
19
+ gem.license = "MIT"
20
+ gem.summary = %Q{Ruby wrapper to run standard-RAxML for Maximum Likelihood tree inference}
21
+ gem.description = %Q{Just a test}
22
+ gem.email = "fer.izquierdo@gmail.com"
23
+ gem.authors = ["Fernando Izquierdo"]
24
+ # dependencies defined in Gemfile
25
+ end
26
+ Jeweler::RubygemsDotOrgTasks.new
27
+
28
+ require 'rake/testtask'
29
+ Rake::TestTask.new(:test) do |test|
30
+ test.libs << 'lib' << 'test'
31
+ test.pattern = 'test/**/test_*.rb'
32
+ test.verbose = true
33
+ end
34
+
35
+ task :default => :test
36
+
37
+ require 'rdoc/task'
38
+ Rake::RDocTask.new do |rdoc|
39
+ version = File.exist?('VERSION') ? File.read('VERSION') : ""
40
+
41
+ rdoc.rdoc_dir = 'rdoc'
42
+ rdoc.title = "bio-raxml #{version}"
43
+ rdoc.rdoc_files.include('README*')
44
+ rdoc.rdoc_files.include('lib/**/*.rb')
45
+ end
data/VERSION ADDED
@@ -0,0 +1 @@
1
+ 0.1.0
@@ -0,0 +1,13 @@
1
+ #!/usr/bin/env ruby
2
+ #
3
+
4
+ load "../lib/bio-raxml/raxml.rb"
5
+
6
+ input = {phylip: "../testdata/lonicera_10taxa.rbcL.phy", name: "test"}
7
+
8
+ puts "Test with #{input.to_s}"
9
+ raxml = BioRaxml::Raxml.new input
10
+
11
+ puts raxml.run_cmd
12
+
13
+ system raxml.run_cmd
@@ -0,0 +1,12 @@
1
+ # Please require your code below, respecting the naming conventions in the
2
+ # bioruby directory tree.
3
+ #
4
+ # For example, say you have a plugin named bio-plugin, the only uncommented
5
+ # line in this file would be
6
+ #
7
+ # require 'bio/bio-plugin/plugin'
8
+ #
9
+ # In this file only require other files. Avoid other source code.
10
+
11
+ require 'bio-raxml/raxml.rb'
12
+
@@ -0,0 +1,11 @@
1
+ module BioRaxml
2
+ class Raxml
3
+ def initialize(opts)
4
+ @phylip = opts[:phylip]
5
+ @name = opts[:name]
6
+ end
7
+ def run_cmd
8
+ cmd = "raxmlHPC-SSE3 -s #{@phylip} -n #{@name} -p 12345 -m GTRGAMMA"
9
+ end
10
+ end
11
+ end
@@ -0,0 +1,18 @@
1
+ require 'rubygems'
2
+ require 'bundler'
3
+ begin
4
+ Bundler.setup(:default, :development)
5
+ rescue Bundler::BundlerError => e
6
+ $stderr.puts e.message
7
+ $stderr.puts "Run `bundle install` to install missing gems"
8
+ exit e.status_code
9
+ end
10
+ require 'test/unit'
11
+ require 'shoulda'
12
+
13
+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
14
+ $LOAD_PATH.unshift(File.dirname(__FILE__))
15
+ require 'bio-raxml'
16
+
17
+ class Test::Unit::TestCase
18
+ end
@@ -0,0 +1,7 @@
1
+ require 'helper'
2
+
3
+ class TestBioRaxml < Test::Unit::TestCase
4
+ should "probably rename this file and start testing for real" do
5
+ flunk "hey buddy, you should probably rename this file and start testing for real"
6
+ end
7
+ end
@@ -0,0 +1,11 @@
1
+ 10 1428
2
+ Lonicera_nervosa atgtcaccacaaacagagactaaagcaagtgttggattcaaagctggtgttaaagagtacaaattgacttattatactcctgagtaccaaaccaaggatactgatatattggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggctgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggngatgctaccacatcgagcccgttgctggagaagaaactcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttggnttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtcgcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggtcgtcccctgttnnnatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccatttttaaagcacaaactgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagacatgatgaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccaccttggctcactattgccgagataatggcctacttcttcacatccaccgcgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagcgttacgtatgtctggtggagatcatattcacgccggtaccgtagtaggtaaacttgaaggggaaagagaaatcactttgggctttgttgatttactgcgtgatgattttattgaaaaggatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgccngctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggnnaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtaaaagctcgtaatgaaggacgtgatcttgctcaggaaggtaatgaaattattcgcgaggcttgcaaatggagcccggaactagctgctgcttgtgaagtatggaaagagatcgtatttaattttgcagcagtggacgttttgtaa
3
+ Lonicera_reticulata --------------------------aagtgttggattcaaagctggtgttaaagagtacaaattgacttattatactcctgagtaccaaaccaaggatactgatatattggcagcattccgagtaactcctcaacccggagttccgcctgaagaagcgggggctgcggtagctgctgaatcttcaaccggtacatggacaactgtgtggaccgatggacttaccagccttgatcgttacaaagggngatgctaccacatcgagcccgttgctggagaagaaactcaatttattgcttatgtagcttacccattagacctttttgaagaaggttctgttactaacatgtttacttctattgtgggtaatgtatttggnttcaaagccctgcgcgctctacgtctggaagatctgcgaatccctgtcgcttatgttaaaactttccaaggcccgcctcatggtatccaagttgagagagataaattgaacaagtacggtcgtcccctgttnnnatgtactattaaacctaaattggggttatctgctaaaaactacggtagggcggtttatgaatgtctacgtggtggacttgattttaccaaagatgatgagaacgtgaactcccaaccatttatgcgttggagagatcgtttcttattttgtgccgaagccatttttaaagcacaaactgaaacaggtgaaatcaaagggcattacttgaatgctactgcaggtacatgtgaagacatgatgaaaagggctgtatttgccagagaattgggagttcctatcgtaatgcacgactacttaacagggggattcactgcaaataccaccttggctcactattgccgagataatggcctacttcttcacatccaccgcgcaatgcatgcagttattgatagacagaagaatcatggtatgcactttcgtgtactagctaaagcgttacgtatgtctggtggagatcatattcacgccggtaccgtagtaggtaaacttgaaggggaaagagaaatcactttgggctttgttgatttactgcgtgatgattttattgaaaaggatcgaagtcgcggtatttatttcactcaagattgggtctctctaccgggtgttctgcccgtggcttcggggggtattcacgtttggcatatgccngctttgaccgagatctttggagatgattccgtcctacagttcggcggaggaactttaggacacccttggnnaaatgcacctggtgccgtagctaatcgagtcgctctagaagcatgtgtaaaagctcgtaatgaaggacgtgatcttgctcaggaaggtaatgaaattattcgcgaggcttgcaaatggagcccggaactagctgctgcttgtgaagtatggaaagagatcgtatttaattttgcagcagtggacgttttggat
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_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:
128
+ rubygems_version: 1.8.10
129
+ signing_key:
130
+ specification_version: 3
131
+ summary: Ruby wrapper to run standard-RAxML for Maximum Likelihood tree inference
132
+ test_files: []