I have whole annotated genomes from five vertebrate species (all fishes) downloaded from NCBI. I want basic comparative stats, such as overall percent sequence divergence, and a simple phylogeny (I know what the topology should be, but I was hoping to date the splits). I am new to whole-genome world, so I unsure how to best proceed. Could the whole genomes be aligned against each other, or is it easier to pick out specific homologous genes/regions? By simply aligning whole genomes of different species, could I simply output a suite of SNPs? I do know that some of the genomes are organized by chromosomes and some by linkage groups.
I suspect it will depend on how distant the genomes are from one another. Fish have been evolving for quite a wile longer than mammals have been (they predated the tetrapods by a few hundred million years). If you have four different species of trout it may be a lot easier than if you have an eel, a trout, a shark, etc...
If I were you, I would start with a few genes, and see what that gets you, first.
I think synteny maps are among the best genome-wide comparative tools. Try to investigate whether this is available online or you need to set it up yourself. Cheers
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