STARRInIGHTS

Strain-based Tree Analysis and Recombinant Region Inference In Genomes from High-Throughput Sequencing projects
by B. Jesse Shapiro and Eric Alm
jesse1 at mit.edu
bshapiro at fas.harvard.edu
STARRInIGHTS STARRInIGHTS is a computational pipeline for inferring homologous recombination breakpoints in populations of closely related bacterial genomes. You can download the complete source code and user's guide here:

User's guide
Download code

A relatively detailed description of the method: Methods description

A short tutorial that will walk you through a toy problem: Download tutorial, toy data set and solutions

You can download the 20-Vibrio genome alignment here: vib20genomes.tar.gz

And the STARRInIGHTS-inferred blocks from this data, here: vib20.STARRI.out.tar.gz