Maximum Likelihood vs Neighbor-Joining
Foley Brian · Figshare · 2013
Comparing Neighbor joining vs Maximum Liklihood phylogenetic tree reconstruction, using the general time reversible model of nucleotide evolution for both, plus a gamma factor for different rates of evolution at different sites, plus allowing a percentage of sites to be held as invariable. The point is that the same data, same model of evolution, produce very similar trees. The real issue with these trees is the saturation of sites as shown in other figures.