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I have computed a phylogenetic tree using an alignement of sequences, and I would like to :

  1. Compare it to the "known" taxonomy (uniprot/ncbi which I know is not the most up to date one) and extract a metric of how "divergent" it is.
  2. [Optional] Visualize the differences (I can probably come up with a solution for that one, but if someone knows of a nice tool to do so ?)

What are the best metrics / tools / methodologies to do such a comparison ?

Thanks !

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Take a look at the ape package in R. It has a function called cophyloplot which allows you to visualize two trees like so:

enter image description here

Which is well described in this question (also the source of the image).

There is also the dist.topo function which produces a metric which describes the topological distance between two phylogenetic trees. I don't know if this is what you mean by "divergent" but I hope it helps.

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