What is PopGenome?
The study of genetic diversity is essential for understanding the nature of evolutionary processes at the molecular level.
The PopGenome library provides data analysis in population genetics and is programmed in the powerful, open-source, statistical computing environment R . Several polymorphism statistics, such as the number of segregating sites and nucleotide or haplotype diversity based FST measurements can be calculated. In addition, PopGenome contributes a lot of neutrality statistics such as the Tajima D and Rozas R2 test. Testing of the significance of these statistics requires generating bootstrap samples from a neutral model using a coalescent approach. To do this PopGenome provides the application of the MS program, which was written by Hudson (2002).
The Sliding window method can be used to scan genetic data with different window and jump sizes. Bayesian methods are becoming increasingly important for population genetic studies and will be implemented in the next release. The PopGenome environment will also have the appropriate data handling and analysis capabilities needed for genome-wide resequencing projects.
- Hudson, R. R. (2002). Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
PopGenome is available on CRAN.