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Can I determine ancestral allele based on phylogenetic tree?

Hi, I have the whole genome of 5 species(S1-S5), and I have constructed the phylogenetic tree of the five species as following. And I now also know the sequences of 4 nodes on the tree(N1-N4) using FastML tool.

My question is:

How can I determine the ancestral alleles for S1? Is N4 sequence the ancestral alleles for S1?

Appreciated for your answer!

                                     |----------S1
                          |----------N4
                          |          |-------------S2
                          |
   |----------------------N3
   |                      |----------S3
   |
   N1
   |                   |-------S4
   |-------------------N2
                       |-------S5
genome alignment gene
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updated by h.mon h.mon • written by wang.yiguan • wang.yiguan

1 answer

As explained on FastML manual:

Can I determine ancestral allele based on phylogenetic tree?

Yes.

Is N4 sequence the ancestral alleles for S1?

Yes (and for S2).

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written by h.mon h.mon

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