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phylogenetic tree with known sampling date prior
0
Entering edit mode
4.1 years ago
hdy • 100
United States

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?

1
Entering edit mode
17 months ago
Brice Sarver ♦ 2.6k
United States

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.