Can I determine ancestral allele based on phylogenetic tree?

Question

[wang.yiguan]

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
  

Answer 1

[h.mon]

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).