How to start the clustering with a MCC tree?

alvinxhan / Phydelity

Inference of putative transmission phylogenetic clusters

GNU Lesser General Public License v3.0

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How to start the clustering with a MCC tree? #6

Open virologist opened 3 years ago

virologist commented 3 years ago

Hi, @alvinxhan

Does the Phydelity compatible with the MCC tree? How to start the clustering with BEAST MCC tree?

Yan

alvinxhan commented 3 years ago

Hi Yan,

Phydelity runs on any tree files in the newick format so as long as you convert your MCC tree from nexus to newick (you can do so easily using figtree), you can use Phydelity. However, I would caution against applying Phydelity to temporal trees as Phydelity operates on estimated patristic distances to infer transmission clusters.