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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for phylopypruner-0.6.5-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 7b5a97683f4457f5c74c27f4b036fee91241a2bacba1bf654e851a40380295bc |
|
MD5 | 2a2c43588e82905551fa8702b5f97f86 |
|
BLAKE2b-256 | ae53cab0d3558c255f7bcc5b74c1cf5cbde2155d45d4612a8afbc34001b2d14e |