ogaraK: A population genetics simulator for malaria and sex theory

Introduction

OgaraK, is a population genetics simulator for modelling the spread of drug resistant malaria. OgaraK is designed to make malaria simulation computationaly tractable as it models infections, not individual parasites. It is made available as free software under the GNU GPL v3.

OgaraK can be run directly from your browser as long as you have a recent version of Java installed.

If you use ogaraK please cite: ogaraK: A population genetics simulator for malaria, Tiago Antao & Ian M. Hastings, Bioinformatics

To run ogaraK, just click
here
[On Google Chrome? You might have to execute the file manually]
Do you have any other problems? Read this

OgaraK can also be run from the command-line. Instructions can be found here.

User guide

A user guide is available.

Supplementary scripts

OgaraK is a simulator and provides no tool for data analysis per se. Simulation data should be analysed with external tools.

While ogaraK is able to export its data into the standard Genepop format, allowing for its output to be analysed by many standard population genetics tools (and, indeed, this is the suggested way to do data analysis), we provide some example scripts in order to help users who might desire to do analysis using scripts.

The scripts are available here.

Development

The development of the application is made openly, using standard tools.

  1. The main development site is hosted in Launchpad, here.
  2. Current development efforts (i.e. the develpment branch), can be found here.

Contact

Any comments or questions? Do not hesistate to contact us.