Utilization of the Scythe C++ open source library for statistical geocomputation in livestock landscape genomics

Understanding genetic basis of adaptation is of key importance, especially to insure food supply for present and future populations. Cultivated plants and livestock animals are subjected to high selection pressure due to climate change, increasing food needs and intensive methods in agriculture. Since adaptation processes are intrinsically linked to landscape, spatial analysis has a role to play in explaining how environmental features shape genetic pool. A research field named landscape genomics combines spatial analysis, population genomics and molecular ecology to provide information about the interaction between landscape features and micro-evolutionary processes. Although association studies may be conducted with standard statistical software, processing such large amount of genetic data provided by highthroughput sequencing technologies is computationally intensive. Therefore we decided develop an open source toolbox dedicated to landscape genomics. The implementation was made easier by using Scythe, an open source C++ library for statistical computation. It supports matrix calculation, provides various statistical functions and allows faster computations than interpreted languages.

Ertz, Olivier
Joost, Stéphane
Tonini, Marj
Published in:
OGRS Symposium Proceedings 2012, 340
Presented at:
The Open Source Geospatial Research and Education Symposium (OGRS), Yverdon-les-Bains, Switzerland, October 24-26, 2012
London, Lulu.com

 Record created 2012-10-31, last modified 2018-03-13

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