tree-based orthology inference
Project description
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
Cite
Our manuscript is still in preparation, it will be posted here once a preprint of the article is available.
© Kocot Lab 2018
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