pyHam: A Tool to Analyze Hierarchical Orthologous Groups (HOGs)

Motivation

pyHam is a library to facilitate the analysis of hierarchical orthologous groups. It also contains a few tools to run standard type of analysis.

Currently, Ham is limited to analyze HOGs that are stored in an orthoXML file. More information on the schema of orthoxml and some examples are available at http://orthoxml.org.

For extended documentation we refer to the docs folder that contain information on common use cases and API documentation of the library.

How to cite pyHam

If you use pyHam in your work, please consider citing:

Clément-Marie Train, Miguel Pignatelli, Adrian Altenhoff, Christophe Dessimoz; iHam and pyHam: visualizing and processing hierarchical orthologous groups, Bioinformatics, bty994, https://doi.org/10.1093/bioinformatics/bty994

Installation

Ham is written in python3 (also compatible with python2), with little external dependencies, i.e. currently ete3, lml, six. The setup script should resolve these dependencies automatically. Consider using pip to install the package directly from a checked out git repo

python -m pip install --upgrade pip
pip install pyham

Example

We prepare a ready-to-use example (see example folder) with few python scripts to use main pyHam features. You just have to run the following command in bash:

python run_hog_queries.py
python run_treeProfile.py
python run_iHam.py

Getting started

We create a small introductory blog post about HOGs and pyHam at http://lab.dessimoz.org/blog/2017/06/29/pyham. We highly recommend you to read it before starting using pyHam.

We also create an ipython notebook to help you with basic uses of pyHam API and embedded tools at http://zoo.cs.ucl.ac.uk/tutorials/tutorial_pyHam_get_started.html.

Table of compatibility

Support for pyHam by various HOG inference resources.

Resource	Species tree format	OrthoXML	SUPPORT
OMA browser_	PhyloXML_ and Newick_	All HOGs_ , or one HOG at a time_	YES
OMA standalone_	PhyloXML and Newick	All HOGs	YES
Ensembl_	Newick_	one HOG at a time	YES
HieranoidDB_	Newick_	one HOG at a time	YES

Documentation

You can the full documentation of pyHam at http://zoo.cs.ucl.ac.uk/doc/pyham/index.html