Is There Any Tool (Or Script) To Detect Signal Conflict Between Two Phylogenetic Trees?
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9.2 years ago
sanchezcavani ▴ 220

I have a plenty of gene trees and a species tree. I was wondering if there is any tool to detect phylogenetic conflict between gene trees and the species tree in batch. Is there any suggestion?

phylogenetics phylogeny tree evolution • 2.4k views
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I think this is related to my recent question: What makes a phylogenetic tree interesting?

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Yes, they are quite similar. However, there is no answer about how to do it in batch. Do you have any suggestions?

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I was thinking to look a bit closer at the supplementary of the nature article in the answer and see if they have included some more information or scripts. The method described in the paper works using the AA sequence as input, so with the trees alone that will not work, btw. where did you get your trees from?

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Btw, what are you after? I wouldn't call this a "conflict" but, it is to be expected that the trees of genes differ somewhat from the "accepted" species tree due to different effects. "conflicts" sounds like as if the observation is not explainable by evolution.

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You are right, I think I should call this phenomenon a different name. I made my gene trees myself.

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