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phylogenetic tree with known sampling date prior

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
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updated by Brice Sarver Brice Sarver • written by hdy hdy

1 answer

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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written by Brice Sarver Brice Sarver

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