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phyloacc / PhyloAcc

PhyloAcc a software to detect the changes of conservation of a genomic region
GNU General Public License v3.0
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Is it necessary to add the ancestor's sequences? #21

Closed Secretloong closed 4 years ago

Secretloong commented 4 years ago

I found the ancestors in your example of the input FASTA file. Is it necessary to use the ancestor's sequences in phyloAcc? If the ancestors were included, would they change the results? If I would like to test only the ancestor's state, parent's branch could be used by phyloP with --branch. How about phyloAcc to test only the ancestor's branch? If users have no Cactus alignments and its estimated ansectors, would you have any suggestions to estimate the ancestors quickly?

Thanks

xyz111131 commented 4 years ago

Nope, you don't need the ancestor sequences. PhyloAcc will estimate the ancestor sequences. I think you were looking at a simulation example where it has the ancestor sequences. The assumption of PhyloAcc is that if an ancestor sequence is accelerated, its children will be accelerated too. So in your case, you could specify the target species as the children of the ancestor branch.

Secretloong commented 4 years ago

Thanks, that makes sense