I have been running my phylogeny tree in MEGA X. My phylogeny tree doesn't seem to have any major differences between species in plain view, but the branches are becoming more clearly divided and each species looks to have major differences in topological view. What happened to my phylogeny tree?
I suspect you are looking at the difference between a "cladogram" with meaningless branch lengths, and a phylogeny where branch lengths are proportional to the distances between the sequences.
I am attaching a treefile, which you should be able to open/import into Mega. Or you can view it with FigTree (free software) or other phylogenetic tree rendering software. Also two views of this same tree, one a cladogram and the other a tree with branch lengths proportional to distances. The cladogram unfortunately also includes a scale bar, which is an error.
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