Question: Msa With Internal Nodes Reconstruction
gravatar for Asaf
8.5 years ago by
Asaf7.2k wrote:


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

phylogenetics multiple • 2.1k views
ADD COMMENTlink modified 6.2 years ago by Biostar ♦♦ 20 • written 8.5 years ago by Asaf7.2k
gravatar for Botond Sipos
8.4 years ago by
Botond Sipos1.7k
United Kingdom
Botond Sipos1.7k wrote:

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

ADD COMMENTlink written 8.4 years ago by Botond Sipos1.7k
gravatar for Michael Kuhn
8.5 years ago by
Michael Kuhn5.0k
EMBL Heidelberg
Michael Kuhn5.0k wrote:

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.

ADD COMMENTlink written 8.5 years ago by Michael Kuhn5.0k

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

ADD REPLYlink written 8.5 years ago by Asaf7.2k
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