Drawing a phylogenetic tree

In the Genome Diversity section, click on the Phylogenetic Tree tool. Once again the appropriate dataset should already be selected automatically. We will use the defaults for most of the options, but for the Minimum Coverage level we'll use the "8" we were looking at in the coverage distribution table. We can be fairly aggressive with this cutoff because this tool looks at the individuals pairwise, rather than all at once (thus a SNP may be usable for comparing two individuals even if it has insufficient coverage in some other individual). For the Data Source option select "estimated genotype", as that works better with low-coverage data. Then click the Execute button.