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-0.8.6-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a7aa6278c4f7c9caf493b964666e0cd858d01bd811f5542db5fc4d63e5d8ec03 |
|
MD5 | fc8261850c77c3f45337fb2dd71cbbb9 |
|
BLAKE2b-256 | 3c0aec10795f90972b203d06278df80efa97aeabba7ae72d5a7473539864be48 |