Adding new low coverage sequences to an existing high quality phylogenetic tree

Question

[hovoh]

Hi,

I have constructed an ML phylogenetic tree from high coverage human Y chromosomal genomes with RAxML. I get SNP lists of every nodes and tips.

Now, I would like to define approximate phylogenetic affiliation of other low coverage genomes, from 1000G phase 3 vcf, for example. The idea is to avoid low coverage genomes' impact during tree consctruction.

Which program could perform this task?

Answer 1

[Jean-Karim Heriche]

You could get a HMM for each tree and calculate the likelihood that your sequences are generated from this model. Then you can rebuild the tree with the new sequences under soft or hard contraints. You can use treebest for this.