docs: Expand documentation for phylo2vec

[lsetiawan]

Need to expand the user facing API documentation in code and expand the jupyter notebook demos to help with potential contributors and increase adoption.

[Neclow]

Anything I can help with?

Otherwise I'll simply assign you and let you test your new agent :)

I do also plan to put a little "primer on phylogenetics" either in the docs or in a wiki which I wrote in my thesis, could be useful to newcomers!

[lsetiawan]

That sounds good. Thanks @Neclow. I'll probably work on this with the agents in the next coming weeks. If you're curious, here's the initial plan that came out: https://github.com/lsetiawan/phylo2vec/blob/docs-improvements/docs-plan/00-overview.md

[Neclow]

Cool! Here's a github link to my thesis just in case: https://github.com/Neclow/phd_thesis. You should be able to compile it in Overleaf. You'll find the primer in 02_Background.tex