Duplicate columns in MSA

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Robert Edgar

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Aug 17, 2021, 10:51:31 AM8/17/21
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How does iqtree handle duplicate columns in the MSA? I'm asking because I want to use a new bootstrapping method that is different from Felsenstein's in some details. Since it is not supported by iqtree, I have implemented my own code for re-sampling columns  with replacement, which  of course produces some duplicate columns. Will iqtree detect and discard the duplicates (which would be wrong in this scenario), or will each column contribute to likelihood (this is what I need)?
Thanks,
Robert.

Minh Bui

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Aug 17, 2021, 6:46:59 PM8/17/21
to IQ-TREE, Robert Edgar
Hi Robert,

All columns (sites) in the alignment will contribute to the likelihood, no matter if they are duplicated or not. Internally, IQ-TREE compresses identical columns into patterns but retain the frequency of occurences and will multiply pattern log-likelihoods with the frequency before taking the sum to get the total log-likelihood. Many software will do this (e.g., RAxML and PhyML). I’m sure that these and other ML software will do the same.

Cheers
Minh


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