Welcome to Mcheza, a selection detection workbench for dominant
Do not email, please use biostars and tag with mcheza
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
- 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 is formally described in
Antao T and Beaumont MA (2011), Mcheza: A workbench to detect selection using dominant markers, Bioinformatics.
Mcheza requires only Java 1.5 or newer (on Linux a C compiler is
also required). This is normally installed by default in most
To run Mcheza click
Note for chrome users: You might have to open the downloaded file
Note for Linux users: Sun's Java implmentation works better than
OpenJDK/IcedTea (the default on most Ubuntu/Debian installs)
Mcheza has a user guide.
Mcheza is licensed under the GPL version 3. The code is available
here. We currently have no documentation for the source.
Questions? Contact us!