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Bioinformatics. 2011 Nov 1;27(21):3070-1. doi: 10.1093/bioinformatics/btr521. Epub 2011 Sep 16.

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data.

Author information

1
MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College, Norfolk Place, London W2 1PG, UK. t.jombart@imperial.ac.uk

Abstract

SUMMARY:

While the R software is becoming a standard for the analysis of genetic data, classical population genetics tools are being challenged by the increasing availability of genomic sequences. Dedicated tools are needed for harnessing the large amount of information generated by next-generation sequencing technologies. We introduce new tools implemented in the adegenet 1.3-1 package for handling and analyzing genome-wide single nucleotide polymorphism (SNP) data. Using a bit-level coding scheme for SNP data and parallelized computation, adegenet enables the analysis of large genome-wide SNPs datasets using standard personal computers.

AVAILABILITY:

adegenet 1.3-1 is available from CRAN: http://cran.r-project.org/web/packages/adegenet/. Information and support including a dedicated forum of discussion can be found on the adegenet website: http://adegenet.r-forge.r-project.org/. adegenet is released with a manual and four tutorials totalling over 300 pages of documentation, and distributed under the GNU General Public Licence (≥2).

CONTACT:

t.jombart@imperial.ac.uk.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
21926124
PMCID:
PMC3198581
DOI:
10.1093/bioinformatics/btr521
[Indexed for MEDLINE]
Free PMC Article

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