Mcheza

Welcome to Mcheza, a selection detection workbench for dominant markers.

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.

Mcheza provides an integrated platform to test dominant markers for selection. The application merges the DFDIST kernel, a widely used Fst-outlier method to detect selection with an intelligent, easy to use interface, some of the features are:

  • DFDIST - The core of Mcheza is a dominant version of a widely used Fst outlier method to detect selection.
  • Support for multitest correction based on false discovery rates (FDR). Multitest correction is fundamental to avoid high overestimation of the percentage of outliers.
  • 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).
  • 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 dfdist.

Mcheza is built using components that are widely used and tested: DFDIST, LOSITAN and Biopython.

Mcheza paper

Mcheza is formally described in Antao T and Beaumont MA (2011), Mcheza: A workbench to detect selection using dominant markers, Bioinformatics.

Run Mcheza!

Mcheza requires only Java 1.5 or newer (on Linux a C compiler is also required). This is normally installed by default in most machines.

To run Mcheza click here
Note for chrome users: You might have to open the downloaded file (mcheza.jnlp)
Note for Linux users: Sun's Java implmentation works better than OpenJDK/IcedTea (the default on most Ubuntu/Debian installs)

User guide

Mcheza has a user guide.

Source code

Mcheza is licensed under the GPL version 3. The code is available here. We currently have no documentation for the source.

Questions? Contact us!