I have SNP data from several cultivars of rice which I have used to produce alignments, but I don't think that the usual models and algorithms used for generating phylogenetic trees are appropriate, because these cultivars are not the result of speciation events and have been interbred in their histories. How can I best calculate and visualize their degree of relatedness?
How does one construct a cladogram of intraspecies relationships?
phylogeny;cladistics;snp