Search genomes for tandem repeats / microsatellites using Phobos

X Plugin

Phobos detects perfect and imperfect microsatellites, minisatellites and DNA-satellites in whole genomes with a high accuracy. It uses a non-probabilistic alignment score as an optimality criterion to decide whether to extend a satellite up or downstream and is able to find alternative alignments with different units for the same satellite.Microsatellites are also known as short tandem repeats (STRs) or simple sequence repeats (SSRs).

By Dr Christoph Mayer

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 sequence and choosing Annotate & Predict - Locate Tandem Repeats with Phobos from the menu. Results are saved as annotations on your sequence.

Before running Phobos 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.


1.0.6 (28 Jun 2010) – Download for Geneious 5.0

Appears in “Annotate and Predict” menu

1.0.4 (04 Nov 2009) – Download

Fixed a bug that caused an imperfect search to be performed when extend exact search was selected


Mayer, Christoph, Phobos 3.3.11, 2006-2010,


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