phylo
Date: 2024-10-10
I just learned of an ACE thingy in phylogenetics. It's a package called BioGeoBears that can simplify something that I was doing through phytools' ACE commands. It's also better because of some DEC stuff. This is really sad. What I learned from this is that there is always a better package out there that can do what you want (unless there isn't in which you write your own).
This BioGeoBears package looks cracked -- good visualizations and DEC is a lot better than normal state reconstruction. D is dispersal where species move about, E is locally extinct from area, and C is cladogenesis where one species splits into two. This allows some species (in my case viruses) to operate within two geographical areas. Actually, as I'm writing this, I'm realizing that this is not needed since one virus sequence very rarely (never) exists in two areas. When people get sequenced, they exist in only one...oh wait. One person can move about thus spreading the same sequence. Confusing...
I will think on this phylogenetic ACE geography stuff a bit more before trying to finish up that project. On another note, college essays have become a lot easier to write. Cya later.