phylogenetic tree with known sampling date prior
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5.4 years ago
hdy ▴ 160

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?

phylogeny phylogenetic tree bayesian • 1.2k views
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5.4 years ago
Brice Sarver ★ 3.7k

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.

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