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Msa With Internal Nodes Reconstruction

Hello,

Given a phylogenetic tree and DNA sequences of orthologous genes in the leaf nodes I would like to reconstruct the DNA sequences in the internal nodes and of course align all the DNA sequences. Do you know a program that does that? some algorithms use trees and can accept trees as their input but I couldn't find a way to retrieve the reconstructed sequences in the internal nodes.

I would appreciate any help

multiple phylogenetics
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updated by Biostar Biostar • written by Asaf Asaf

2 answers

The PRANK and webPRANK aligners reports the inferred ancestral sequences on request.

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written by Botond Sipos Botond Sipos

I've never done this, but the keyword you're looking for is ancestral sequence reconstruction. That will lead to papers with method sections and some informative slides (pdf link). There's even a webserver for this: FASTML.

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written by Michael Kuhn Michael Kuhn

Thanks, but these algorithms assume a MSA, I think that the reconstruction and the MSA should be computed together and influence one another.

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written by Asaf Asaf

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