Advance Access publication September 16, 2011 | Thibaut Jombart and Ismaïl Ahmed
The article introduces new tools in the *adegene 1.3-1* package for handling and analyzing genome-wide single nucleotide polymorphism (SNP) data. These tools are designed to address the challenges posed by the increasing availability of genomic sequences, which require more powerful computing resources and specialized tools. The *adegene 1.3-1* package uses a bit-level coding scheme for SNP data and parallelized computation to enable the analysis of large genome-wide SNP datasets on standard personal computers. The package includes a new class, *genlight*, which efficiently represents biallelic SNPs using a single bit, significantly reducing memory usage. The package also supports parallel computation, making it suitable for large datasets. An example using discriminant analysis of principal components (DAPC) demonstrates how the package can identify structuring alleles from genomic data with minimal computing resources. The *adegene 1.3-1* package is available on CRAN and provides comprehensive documentation and support.The article introduces new tools in the *adegene 1.3-1* package for handling and analyzing genome-wide single nucleotide polymorphism (SNP) data. These tools are designed to address the challenges posed by the increasing availability of genomic sequences, which require more powerful computing resources and specialized tools. The *adegene 1.3-1* package uses a bit-level coding scheme for SNP data and parallelized computation to enable the analysis of large genome-wide SNP datasets on standard personal computers. The package includes a new class, *genlight*, which efficiently represents biallelic SNPs using a single bit, significantly reducing memory usage. The package also supports parallel computation, making it suitable for large datasets. An example using discriminant analysis of principal components (DAPC) demonstrates how the package can identify structuring alleles from genomic data with minimal computing resources. The *adegene 1.3-1* package is available on CRAN and provides comprehensive documentation and support.