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.

On newer macOS computers you will need to run the Phobos executable by itself at least once before Geneious Prime will be able to use it. To do this:

Locate the Phobos executable in Finder
Right-click on it and select Open
If macOS shows you a warning, select Open or Continue
Phobos will open a terminal and run. You can now close the terminal and use Phobos from Geneious Prime.

History

1.0 (12 Oct 2012) – Download

Citing

Mayer, Christoph, Phobos 3.3.11, 2006-2010,

Polymorphic SSRs