Am working with genome sequences of A. thaliana species - and trying to derive the sequence of the recent ancestor of A.thaliana.
Looking at the consensus of multiple Thaliana strains at a given position and comparing it to that of Lyrata I can think of some possibilities to determine the base of the recent ancestor of A.thaliana.
I am looking for some feedback from the community, leads to literature that use algorithms to identify not the most recent common ancestor but the just the recent ancestor of the species.
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written
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ngsgene
2 answers
I think you can use codeml to generate the ancestor sequence from your group of thaliana sequences. You'll need the phylogeny of sequences in newick format though.
You're welcome. I hope you enjoy the biostar community and continue to participate here.
I don't know how far you want to go into the subject, but I would suggest Ancestral Sequence Reconstruction by David Liberles (http://www.oxfordscholarship.com/oso/public/content/biology/9780199299188/toc.html). Chapter 4 onwards goes into computational methods. If this goes in to deep there are lots of papers, just google ancestral sequence reconstruction.
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It's not clear to me what you mean by recent ancestor as opposed to recent common ancestor. Isn't an ancestor of a particular species not always common to this species and another species?
What I have been thinking is A.thaliana & A.lyrata would have a recent common ancestor while I am more inclined to know the ancestor of A.thaliana - so it shouldn't be 'common' - perhaps there's another apt word for it.
It should be recent common ancestor - for the multiple strains of Thaliana it is a 'recent common ancestor'