<scp>aflpdat</scp>: a collection of <scp>r</scp> functions for convenient handling of AFLP data

TLDR

aflpdat is an R package that simplifies handling of dominant genotypic data. It converts tab‑separated AFLP data into formats for Arlequin, STRUCTURE, Treecon, PAUP, and Hickory, computes polymorphic marker proportions, estimates gene diversity with bootstrap confidence intervals, and generates summary tables of marker frequencies. The package is available for download at http://www.nhm.uio.no/ncb/.

Abstract

Abstract aflpdat is a collection of 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: arlequin , structure , treecon , paup and 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. aflpdat can be downloaded from http://www.nhm.uio.no/ncb/ .