How to build a frequency matrix of alleles based on SSR markers to calculate UPGMA dendrogram?

18 November 2019 1 10K Report

When you got the raw data from an SSR marker survey it is presented as length (number of base pairs) of alleles. Typically, a matrix with samples in rows and allele length in columns. However, how do I build a matrix for calculating neighbour joining or UPGMA dendrogram from these lengths? As I understand I must “translate” the data to binary 1/0 data?

Justin H. Bohling

The POPPR and APE packages in R work great for this as well, especially for co-dominant SSRs.

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