Software

This page introduces my computer code developed and published for the research community since 2015.

1. Population genomics

1.1. Detection of horizontal gene co-transfer between bacteria

GeneMates

The latest version: v0.2.2, which was released on 21 March 2020. (Documentation)

This R package implements my network approach for the detection of intra-species horizontal gene co-transfer (HGcoT) between bacteria. A manuscript is preparing for it. GeneMates takes as input bacterial whole-genome sequencing (WGS) data (in the forms of short reads and/or genome assemblies) and creates networks showing evidence of HGcoT at the allele level. This package can also be used for testing for allele-to-allele associations controlling for bacterial population structure. The following list introduces GeneMates functions that are frequently used in my experience.