Thank you very much for the pointers,

"Mammalian genomes are so much bigger than bacterial genomes that you could run into computational issues"

Yes this is the main concern for us now Can the tools mentioned in my primery thread, largely used for whole genome phylogenetic analysis of prokaryotes, can be used for large mammalian genomes?

"but the main problem is that across mammalian species, the fraction of the genome that contains relevant phylogenetic information may be small so your alignment could be swamped by the alignment of irrelevant portions of the genomes. This could be less of an issue if you're trying to align genomes of individuals from the same species or genomes of closely related species"

You are abosolutely right here I am indeed comparing genomes from same species, so the problem is minimized, to this end

"but you're not telling us what it is you're trying to do so it is impossible to be specific"

Here's our objective, I have several Opossum (Didelphis Virginiana) genomes sequenced and assembled. Now I want to perform "Whole Genome Phylogeny Analysis".

To elaborate, Most of the phologeny analysis, involves either 16s rRNA (bacteria and archaea), 18s (Lower eukaryotes). There are many generally established mammalian evolutionary phylogenies and a number of single-gene phylogeny methods for mammalian species.

However, I want to perform the "whole genome phylogenetic analysis", rather than single-gene phylogeny methods.

I found this paper, which is closest to my objectives,

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761373/ But are there any more such tools or methods? Is it even feasible (at this time) to perform this analysis for large genomes? Note: Computational resource is not an issue