assembly based phylogeny

Question

[samuel.a.odonnell]

Hi everyone;

I have approximately 600 genomes from a variety of species within a genus with a genome size ~30-40Mb. My goal is to use these genomes, without annotation, to generate a phylogenomic tree. I have had a bit of a look for tools to perform this and came across SANS serif and JolyTree but I cannot manage to get them to work (sans-serif has issues I do not understand and JolyTree requires several dependencies with their own dependencies which contain complications at each installation step)

Other than those two I did not find any other options.

Does anyone know of a tool or pipeline/ had experience with generating tree from assemblies?

Cheers

Samuel

Answer 1

[shelkmike]

You can analyse these genomes with BUSCO and then apply the BUSCO_phylogenomics pipeline https://github.com/jamiemcg/BUSCO_phylogenomics. It builds a tree based on sequences of BUSCO genes.