Mcheza: a workbench to detect selection using dominant markers.

Tiago Rodrigues Antao; Mark A. Beaumont

doi:10.1093/bioinformatics/btr253

Mcheza: a workbench to detect selection using dominant markers.

Tiago Rodrigues Antao, Mark A. Beaumont

Liverpool School of Tropical Medicine

Liverpool School of Tropical Medicine

Research output: Contribution to journal › Article › peer-review

78 Citations (Scopus)

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.

Original language	English
Article number	btr253
Pages (from-to)	1717-1718
Number of pages	2
Journal	Bioinformatics
Volume	27
Issue number	12
DOIs	https://doi.org/10.1093/bioinformatics/btr253
Publication status	Published - 15 Jun 2011

Access to Document

10.1093/bioinformatics/btr253

Cite this

@article{20d8ea69e8ab42809d0318086677a118,

title = "Mcheza: a workbench to detect selection using dominant markers.",

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.",

author = "\{Rodrigues Antao\}, Tiago and Beaumont, \{Mark A.\}",

year = "2011",

month = jun,

day = "15",

doi = "10.1093/bioinformatics/btr253",

language = "English",

volume = "27",

pages = "1717--1718",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "12",

}

TY - JOUR

T1 - Mcheza: a workbench to detect selection using dominant markers.

AU - Rodrigues Antao, Tiago

AU - Beaumont, Mark A.

PY - 2011/6/15

Y1 - 2011/6/15

N2 - 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.

AB - 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.

U2 - 10.1093/bioinformatics/btr253

DO - 10.1093/bioinformatics/btr253

M3 - Article

SN - 1367-4803

VL - 27

SP - 1717

EP - 1718

JO - Bioinformatics

JF - Bioinformatics

IS - 12

M1 - btr253

ER -

Mcheza: a workbench to detect selection using dominant markers.

Abstract

Access to Document

Fingerprint

Cite this