/BowfinGOPhylogeny

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BowfinGOPhylogeny - Bowfin Gene Order Phylogeny

Binder

BowfinGOPhylogeny is a repository to build distance-based gene-order phylogenies, based on the approach we used in the bowfin genome paper. The notebook shows how to use the python3 scripts stored in modules/ in conjonction with standard tree building tools to reproduce the 13 ray-finned fish phylogeny we presented.

In addition, we provide all source data used for genome comparisons shown in the bowfin genome paper. See data/README.md for details.

Quick start with binder

Click the launch binder badge above to directly open and interactively run the notebook.

Running locally

This is a short guide to setting up the notebook environment with conda. If you do not wish to use conda you will need to install the dependencies listed in binder/environment.yaml to run the notebook.

  • Clone the repository and go to the root folder
git clone https://github.com/DyogenIBENS/BowfinGOPhylogeny.git
cd BowfinGOPhylogeny
  • Create the conda environment using mamba
conda install -c conda-forge mamba
mamba env create -f binder/environment.yaml
  • Install the conda extension for jupyter in your base environment - or in any environment where you want to run jupyter (if you do not have jupyter you should install it first with mamba install -c anaconda jupyter).
mamba install nb_conda_kernels
  • Launch the notebook and then interactively select the bowfin_go kernel in the list
jupyter notebook

Authors

  • Elise Parey
  • Alexandra Louis
  • Ingo Braasch
  • Hugues Roest Crollius
  • Camille Berthelot

License

This code may be freely distributed and modified under the terms of the GNU General Public License version 3 (GPL v3) and the CeCILL licence version 2 of the CNRS: