Conclusion
GenAPoPop provide a user-friendly, multi-operating systems, efficient mass processing way to analyse autopolyploid (including diploid) genotypings with a special focus on interpreting the genetic diversity and its structure within and between populations in regards with their reproductive modes. It especially allows computing genotypic indices to analyse clonal heterogeneity and clonal evenness for polyploids due to repeated multilocus genotypes (MLGs) in samples. It includes an extension of the robust and efficient ClonEstiMate Bayesian method to quantitatively infer joint rates of clonality, selfing and allogamy using populations genotyped at two-time steps. It facilitates the interpretation of genetic diversity in partially clonal, partially selfing autopolyploid populations with no or very-limited double reduction. It has no vocation to include or encompass all methods and population genetic indices that can be computed when analysing autopolyploid genotypings. This is why it allows exporting datasets in format that can be uploaded in other software like Spagedi (Hardy & Vekemans 2002), Genodive (Meirmans 2020) and Polygene (Huang et al. 2020). We thus warmly recommend users to use GenAPoPop in complement to other dedicated analyses that can be found in these other softwares, depending on the tackled questions. GenAPoPop also answers the need of a population genetic analysing software for autopolyploid dataset with confident allele dosage that will come growing with the new genotyping-by-sequencing methods with individually tagged sample and locus. It finally answers the need of a user-friendly software for practical course that doesn’t need teaching command-lines or scripting languages as a prior to introduce students to population genetics for polyploid species and to the genetic consequences of reproductive modes on the genetic diversity and structure of populations.