Which R packages are fit for calculating distances and make phylogenetic trees from VCF files?

Question

[rimgubaev]

Hello everyone! Please suggest some R packages for calculating distances and make phylogenetic trees from VCF files. I am searching for package with clear manual/tutorial and broad number of methods to calculate genetic distances and tree building, bootstrapping. Thank you.

[Benn]

Maybe this tutorial can help, there is a hcl tree produced somewhere in the middle.