I have a concatenated alignment of candidate phyla ribosomal proteins [4 markers]. I did this by generating each of the alignments separately and then literally just concatenated the strings together for each organism. Anyways, I've been doing some digging and most sources say that UPGMA is a terrible method for phylogenetic reconstruction.
I'm attaching the neighbor joining and UPGMA results side by side. The UPGMA makes MUCH more sense in terms of taxonomy where similar taxa are next to each other and the outgroups are off on there own. This is not the case with the neighbor joining.
Why is neighbor-joining better and why should I not trust the UPGMA results even though they are more consistent with a priori taxonomy assignments?