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pcadapt software


pcadapt
pcadapt implements a genome scan for detecting genes involved in local adaptation. The software is available as the R pcadapt package. On CRAN, there is a tutorial that explains how to perform a genome scan using the R package. In the past, a C software was also available.  An archive to download the C software is available below but we rather recommand to use the R package.

The last version of PCAdapt fast (updated February, 11, 2016, deprecated use the R package instead)
A brief history of pcadapt
The first version was based on a hierarchical Bayesian factor model (Duforet-Frebourg et al. 2014). The second and much more rapid version used Principal Component Analysis and the communality statistic to look for candidate SNPs (Duforet-Frebourg et al. 2016). The current version uses Principal Component Analysis and the Mahalanobis distance, which provides a better ranking of candidate SNPs than the communality statistic especially when there is hierarchical structure (Luu, Bazin and Blum, 2016).


References
K Luu, E Bazin and MGB Blum. pcadapt: an R package for performing genome scans for selection based on principal component analysis. biorXiv:10.1101/056135 (2016)

Duforet-Frebourg N, K Luu, G Laval, E Bazin, MGB Blum. Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data. Molecular Biology and Evolution 33:1082-1093 (2016) in press

Duforet-Frebourg N, E Bazin, MGB Blum. Genome scans for detecting footprints of local adaptation using a Bayesian factor model. Molecular Biology and Evolution, 31:2483-2495 (2014)

Contact
Michael BLUM <michael_dot_blum_at_imag_dot_fr>
Keurcien LUU <keurcien_dot_luu_at_imag_dot_fr>