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.
Computational Cell Biology, Heinrich-Heine-Universität Düsseldorf
- Linux / WIndows /MacOsX
- R package
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Mol Biol Evol. 2014 Jul;31(7):1929-36. doi: 10.1093/molbev/msu136. Epub 2014 Apr 16.
PopGenome: an efficient Swiss army knife for population genomic analyses in R.
Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ