Question: Msa With Internal Nodes Reconstruction
2
gravatar for Asaf
7.6 years ago by
Asaf5.5k
Israel
Asaf5.5k wrote:

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

phylogenetics multiple • 1.8k views
ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 7.6 years ago by Asaf5.5k
1
gravatar for Botond Sipos
7.5 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 7.5 years ago by Botond Sipos1.7k
0
gravatar for Michael Kuhn
7.6 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 7.6 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 7.6 years ago by Asaf5.5k
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