Phylogenetic analysis through sliding windows in VCF

Question

[hollymolly]

Hello I am now looking for a program that does phylogenetic analysis on VCF files. Of course, there are many programs that can perform phylogeny analysis, but what I want to study now is to divide the genes of individuals of various animal species into sections with sliding windows and find out where the differences between species occur in the genes. Is there a program that can use a VCF file to section it in sliding windows and then form a phylogenetic tree? Or, tell us about the protocols you use for these analyses. I don't know anything yet I'm new to this field so I need some help!

[dthorbur]

I've not heard of a tool that will do both the sliding windows and phylogenetic trees, so you may have to break up the analysis into multiple steps.

Here are two tools for phylogenies based on VCF files: SNPRelate and SNPhylo.

However, I think you would have to subset the VCF to only contain one window at a time. An alternative approach would be emitting a MSA fasta for each window and using conventional phylogenetic tools like RAxML, which shouldn't be too challenging.