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A tool to analyse Hierarchical Orthologous Groups (HOGs)

Project description

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.

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

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.

DOCUMENTATION

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

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pyham-1.0.3-py2.py3-none-any.whl (33.0 kB) Copy SHA256 hash SHA256 Wheel py2.py3 May 15, 2018
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