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Mcheza: a workbench to detect selection using dominant markers.

Rodrigues Antao, Tiago and Beaumont, Mark A. (2011) 'Mcheza: a workbench to detect selection using dominant markers.'. Bioinformatics (Oxford, England), Vol 27, Issue 12, pp. 1717-8.

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Abstract

Motivation: Dominant markers (DArTs and AFLPs) are commonly used for genetic analysis in the fields of evolutionary genetics, ecology and conservation of genetic resources. The recent prominence of these markers has coincided with renewed interest in detecting the effects of local selection and adaptation at the level of the genome.

Results: We present Mcheza, an application for detecting loci under selection based on a well-evaluated FST-outlier method. The application allows robust estimates to be made of model parameters (e.g. genome-wide average, neutral FST), provides data import and export functions, iterative contour smoothing and generation of graphics in an easy to use graphical user interface with a computation engine that supports multicore processors for enhanced performance. Mcheza also provides functionality to mitigate common analytical errors when scanning for loci under selection.

Availability: Mcheza is freely available under GPL version 3 from http://popgen.eu/soft/mcheza.

Item Type: Article
Uncontrolled Keywords: Software; Bioinformatics; Genetic analysis
Subjects: QU Biochemistry > QU 26.5 Informatics. Automatic data processing. Computers
QU Biochemistry > Genetics > QU 450 General Works
Faculty: Department: Groups (2002 - 2012) > Molecular & Biochemical Parasitology Group
Digital Object Identifer (DOI): https://doi.org/10.1093/bioinformatics/btr253
Related URLs:
Depositing User: Mary Creegan
Date Deposited: 12 Aug 2011 09:00
Last Modified: 06 Feb 2018 13:03
URI: https://archive.lstmed.ac.uk/id/eprint/2279

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