Msa With Internal Nodes Reconstruction

Question

[Asaf]

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

Answer 1

[Botond Sipos]

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

Answer 2

[Michael Kuhn]

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.

[Asaf]

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