This tutorial on GBrowse syn was taught by Sheldon McKay as part of the 2013 GMOD Summer School.
The starting image for this tutorial is 2013 GMOD start day 4 (ami-3f7c0456). It can be run as a micro or small instance.
GBrowse_syn is a GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It is included with the standard GBrowse package (version 1.69 and later).
The focus of the section of the course is on dealing with alignment or synteny data and using GBrowse_syn. However, how to generate whole genome alignments, identify orthologous regions, etc., are the subject of considerable interest, so some background reading is listed below:
There is detailed documentation on the GMOD wiki for how to install, configure and use GBrowse_syn. To get started, browse these pages: