In this guide, we will explain how to get the species phylogenetic tree using just the draft genomes (genomes that still don't have the annotations yet). For data, we will use the sequenced legume genomes. You will need the following programs installed and access to a large cluster (we use Condo in this exercise).
Like mentioned before, we will use the sequenced legume genomes for this purpose. Not all genomes had gene predictions hence we will predict the BUSCO genes before we construct phylogentic tree.
The data can be downloaded from using the commands: