I think understanding what you want to base the phylogeny on is probably an even more important question. If you want to align the entire genomes of these 144 species and construct phylogeny then I do not know if that would be feasible at all. Not that I am an expert in phylogeny, but the amount of noise introduced within phylogenetic inferences is directly proportional to the number of species you use in making the tree, and, in my opinion, 144 is a very large number. You would first need to know exactly which regions of the genomes are you claiming to be potentially conserved/similar across all 144 species that you could base your phylogeny on.