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AADavin / ALEtutorial

A tutorial on Phylogenetic Reconciliations using ALE
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Can a single gene tree be used for reconcilation? #2

Open Mia1349 opened 3 months ago

Mia1349 commented 3 months ago

Thank you for the tutorial. The GBE paper was extremely informative and greatly enhanced my understanding of reconciliation processes.

I am wondering if a single gene tree can be used for reconciliation. I have compiled a list of gene trees constructed using a distance-based method therefore I do not have a distrubution of bootstrap trees. Would it make sense to reconcile these trees with a species tree? Additionally, would the results obtained from such a reconciliation be meaningful?

Best, Mia

AADavin commented 3 months ago

Hi Mia! Glad you found the explanation useful. You can use a single gene tree for the reconciliation, there is absolutely no problem with that. The only issue here is that ALE won't be able to "improve" the topology of the gene tree, and it will use the exact topology that you use as input. Whether the results are meaningful or not will depend a lot on your dataset and I can't really say without some more background. Hope that helps!