HoMer: Horizontal Multi-Gene Transfer Inference

HoMer (short for “Horizontal Multi-gene transfer inference”) is a software package for inferring instances of horizontal multi-gene transfer (HMGT) during the evolutionary history of a collection of microbial species/strains. An HMGT occurs when multiple genes are horizontally transferred in single horizontal transfer event. HoMer takes as input a rooted species tree, gene ordering information for the species/genomes (leaves) represented in the species tree, and rooted gene trees for all gene families (with at least three genes each) present in the species/genomes under consideration. The software outputs a list of inferred HMGTs for each donor-recipient pair on the species tree, where donors/recipients can be leaves (i.e., given genomes) or internal (i.e., ancestral) edges on the species tree.

HoMer is written in Python and requires version 3.0 or greater. The implementation also assumes that ETE 3 toolkit is already installed. ETE toolkit is available freely from etetoolkit.org. Further technical details appear in the manual and in the paper cited below.

HoMer was implemented by Lina Kloub and is available open source under GNU GPL. Python Code, along with pre-compiled auxiliary C/C++ code (for Linux and macOS), and a user manual are available below.

The Aeromonas dataset used in this research and the list of HMGTs inferred on this dataset are also available below.

This software can be cited as follows:

  • Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes
    Lina Kloub, Sean Gosselin, Matthew Fullmer, Joerg Graf, J. Peter Gogarten, Mukul S. Bansal
    Under review

Funding: Development of the software resource(s) available from this webpage was funded in part by U.S. National Science Foundation award MCB 1616514.

Contact: Please feel free to contact Mukul Bansal (mukul.bansal@uconn.edu) if you have any questions, concerns, or suggestions.