phylogenetic tree with known sampling date prior

Question

[hdy]

I have an experiment which provides sequencing data for the bacteria at different sample time point. Normally when plotting the phylogenetic tree after multi-sequence alignment, the resulted tree is a representation of all the genomes collected without the useful prior knowledge of the sampling date. Is there a way to incorporate this information into the phylogenetic tree?

Answer 1

[Brice Sarver]

You'll want to make sure you are actually estimating a tree, not just plotting a dendrogram or something that is not phylogenetic.

One way to do this, in Python, is to use DendroPy for non-contemporaneous dating. Check out the example here for use on summary trees.