part d assigning genotypes for codominant alleles

In version 2.0, tools for genomic data were introduced (Zhian N Kamvar, Brooks, and Grünwald 2015). With poppr you can also quickly calculate Bruvo’s distance, the index of association, and easily determine which multilocus genotypes are shared across populations. Poppr has the ability to bootstrap, clone-censor, and subset data sets. The real power of poppr is in the data manipulation and analytic tools. This means that anything you can analyze in adegenet can be further analyzed with poppr. To avoid creating yet another file format that is specific to a program, poppr was created on the backbone of the popular R package adegenet and can take all the file formats that adegenet can take (Genpop, Genetix, Fstat, and Structure) and newly introduces compatibility with GenAlEx formatted files (exported to CSV). Poppr allows analysis of haploid and diploid dominant/co-dominant marker data including microsatellites, Single Nucleotide Polymorphisms (SNP), and Amplified Fragment Length Polymorphisms (AFLP). Poppr is designed to make analysis of populations with mixed reproductive modes more streamlined and user friendly so that the researcher using it can focus on data analysis and interpretation.

Furthermore, a typical analysis often involves switching between many programs, and converting data to each specific format. There are several stand-alone programs that can handle these types of data sets, but they are often platform specific and often only accept specific data types. While there are many R packages in CRAN and other repositories with tools for population genetic analyses, few are appropriate for populations with mixed modes of reproduction.

Poppr is an R package with convenient functions for analysis of genetic data with mixed modes of reproduction including sexual and clonal reproduction.

Part d assigning genotypes for codominant alleles