Calculate sequence diversitySource:
This performs basic diversity analyses on genetic data, specifically, average pairwise divergence (\(\pi\)), segregating sites, estimated mutation rate (\(\theta\), or \(4N\mu\)), and Tajima's D can be calculated, as well as sliding windows of diversity.
seqDiversity( tasObj, startSite = 0, endSite = NULL, slidingWindowAnalysis = FALSE, stepSize = 100, windowSize = 500 )
An object of class
TasselGenotypePenotypethat contains a genotype table.
End site. Defaults to the maximum index of markers.
Do you want to analyze diversity in a sliding window? Defaults to