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Last pushed: 5 months ago
Short Description
Command line app for Iroki, a phylogenetic tree customization program.
Full Description


Command line app and library code for Iroki, a phylogenetic tree
customization program.


Iroki is research software. If you use Iroki, please cite the Iroki preprint:

Moore RM, Harrison AO, McAllister SM , Marine RL, Chan CS, and Wommack KE. 2017. Iroki: automatic customization for phylogenetic trees. bioRxiv doi:10.1101/106138


For in depth docs and examples, please see the Iroki wiki page.


Using the web app

Iroki has a web app ( The code for that is also on GitHub.

Running with Docker

See the wiki.

Use the command line app with RubyGems

If you already have a working Ruby environment, run this

$ gem install iroki

Then type which iroki and you should see something like this


If so, you are good to go!

To use the library code

Add this line to your application's Gemfile:

gem 'iroki'

And then execute:

$ bundle

Or install it yourself as:

$ gem install iroki

Other programs

Newick format to PhyloXML

  • exe/newick_to_phyloxml

This will be installed when you run gem install iroki.

Usage: newick_to_phyloxml tree.newick > tree.phyloxml

Note: No specs for this as of yet.


After checking out the repo, run bin/setup to install
dependencies. Then, run rake spec to run the tests. You can also run
bin/console for an interactive prompt that will allow you to

To install this gem onto your local machine, run bundle exec rake install. To release a new version, update the version number in
version.rb, and then run bundle exec rake release, which will
create a git tag for the version, push git commits and tags, and push
the .gem file to


Bug reports and pull requests are welcome on GitHub at This project is intended to
be a safe, welcoming space for collaboration, and contributors are
expected to adhere to the
Contributor Covenant code of

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