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LOSITAN is a selection detection workbench based on the fdist Fst outlier methods. It runs in Windows, Mac OS X and Linux and is able to use modern multi-core processor architectures.

Background

Understanding the contribution of selection and molecular adaptation in shaping genome wide variation has many applications ranging from human health to conservation of endangered species. Among the many selection detection strategies, Fst outlier approaches are still widely used, most notably the method which is implemented in the fdist program.

See Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London B 263: 1619-1626.

If you use LOSITAN please cite the above paper and our application note: LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method. Tiago Antao, Ana Lopes, Ricardo J Lopes, Albano Beja-Pereira, Gordon Luikart BMC Bioinformatics 2008, 9:323.

Advantages

  • Java Web Start application with an easy to use interface, directly usable from the web.

  • Data import in Genepop format

  • Data export to R or commonly used spreadsheet software.

  • Ability to choose which populations and/or loci are studied.

  • Approximating average neutral Fst by removing potential selected loci.

  • Approximating average simulated Fst to the average value found on the real dataset even when the experimental conditions are far from the ones where the theoretical formula holds (e.g. low number of demes or the usage of the stepwise mutation model, common in microsatellite markers).

  • Iterative smoothing of confidence interval contours.

  • Generation of publication quality graphics in several formats (PNG, SVG and PDF).

  • Ability to use multiple CPU cores when running fdist.

  • Automatic and transparent download of the latest version of fdist.

Help

We hope these videos will be more helpful than a text manual to get people working on the program.

Tutorial 1 Tutorial 2

We also make available a bare bones script to help you load and process data in R.

Download Java

Just click the icon above. This opens a link that will download and install the software automatically. Java can be also downloaded

System Requirements

Windows: At least Windows 2000 and Java 1.6.

Mac OS X: 10.4 (Tiger) and Java 1.5 (You might need to upgrade the default 1.4 Java on Tiger).

Linux: Java 1.6 and the free GNU C compiler (usualy available in most distributions).

Developer's corner

This program is free software. You can download the source code, request enhancements and report bugs here.

We also make a source zip available if you don't to download from our development site.

The code used in Lositan was donated to the Biopython population genetics module.

Supporters

This was made possible with the support of FCT (Fundação para a Cíência e a Tecnologia).

Tropical Medicine logo CIBIO logo FCT logo