Polymorphic SSRs

Find polymorphic tandem repeats in alignments using Phobos

Polymorphic SSRs Plugin

This plugin detects tandem repeats in aligned sequences using Phobos and then compares them to identify repeats which vary in length between the sequences. Any of these polymorphic SSRs are then annotated on the consensus sequence of the alignment.

Quick Start

Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).

Once installed, run the plugin by selecting a nucleotide alignment and choosing Annotate & Predict - Find Polymorphic SSRs from the menu. Results are saved as annotations on the sequences.

Before running the plugin you will need to set The Phobos executable to point to your copy of Phobos. Phobos must be downloaded from the official website. Commercial users require a license from the author.

History

1.0 (12 Oct 2012) – Download

Citing

Mayer, Christoph, Phobos 3.3.11, 2006-2010,

Polymorphic SSRs