How do you make a tree file in R using a fasta MSA?

Question

[DNAngel]

I have phylip files and fasta files of MSA that I want to convert into phylo objects in R for further analysis. I've read up on ape, phylotools, phytools, and ggtree, but none of those seem to have an option of actually making a phylo object - they just want you to import your .tre or .nwk files already created before.

There''s gotta be a way to make these in R?

[Joe]

That’s because tools like ggtree are for visualising, not calculating, trees.

Is there any particular reason you want to calculate the tree in R? Most of the best tools are standalone programs.