A good tutorial for eukaryotic phylogeny?

Question

[predeus]

Hello all,

I was wondering if you know of a good tutorial showing how to make a simple phylogeny of several eukaryotic species?

Basically, as far as I understand, you start with an annotated genome, and need to 1) identify single-copy orthologues; 2) do multiple alignment; 3) select the "good" parts of the alignment, and 4) build the tree

However, there are tricky parts about quickly vs slowly evolving genes etc. So if somebody can point me in the right direction I would be very grateful.

Answer 1

[Vitis]

I came across this paper recently about reconstruction of genome phylogeny for a butterfly species radiation. The methodology might be interesting for you to take a look. They used long reads assembled genomic sequences and Cactus to align the genomes, then created gene trees and species trees, etc.

https://www.biorxiv.org/content/10.1101/466292v1

[predeus]

Thank you, that's an interesting approach. I need to compare quite distant species though, so I don't think alignment in nucleotide space would be very useful.