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aflpdat: a collection of r functions for convenient handling of AFLP data
- EHRICH, DOROTHEE
- Molecular ecology notes 2006 v.6 no.3 pp. 603-604
- Carya, amplified fragment length polymorphism, confidence interval, genes, genetic markers
- [smallcapital aflpdat] is a collection of [smallcapital R] functions that facilitates the handling of dominant genotypic data. It converts data from a standard tab-separated table to the input formats of the following programs: [smallcapital arlequin], [smallcapital structure], [smallcapital treecon], [smallcapital paup] and [smallcapital hickory]. In addition, it calculates the proportion of polymorphic markers in each population, and estimates gene diversity as the average proportion of pairwise differences between individuals with confidence intervals based on bootstrapping across markers. It also produces summary tables of marker frequencies and the presence or absence of markers in each population. [smallcapital aflpdat] can be downloaded from http://www.nhm.uio.no/ncb/.