phylopypruner 0.8.1

tree-based orthology inference

What is PhyloPyPruner?

PhyloPyPruner is a Python package for refining the output of a graph-based orthology inference approach such as OrthoMCL, OrthoFinder or HaMStR. Similar to other tree-based orthology inference methods (e.g., PhyloTreePruner, UPhO, Agalma and Phylogenomic Dataset Reconstruction), it uses phylogenetic trees in order to obtain genes that are 1:1 orthologous. In addition to filters and algorithms seen in pre-existing tools, this package provides new methods for differentiating contamination-like sequences from paralogs.

PhyloPyPruner is under active development and I would appreciate it if you try this software on your own data and leave feedback.

Figure 1. A rough overview of a tree-based orthology inference approach.

Quick installation

The easiest way to install PhyloPyPruner is by using the package manager for Python, pip:

pip install phylopypruner # install for all users
pip install --user phylopypruner # install for the current user only

Once installed, the program is located within $HOME/.local/bin. Depending on your OS, you might have to add the directory to your $PATH to avoid typing the entire path. Once in your path, you run the program like this:

phylopypruner

Documentation

1. About PhyloPyPruner
2. Tutorial
3. Installation
4. Input data
5. Output files
6. Methods
7. Options

Cite

Our manuscript is still in preparation, it will be posted here once a preprint of the article is available.

© Kocot Lab 2018