I am currently comparing the orthologs of a single protein, doing multiple alignments and constructing a phylogram using MEGA7. I am seeing several zero-length branches (three out of seven branches). I search around online and see that this is assumed to be because the "descendants" have the same characteristics as the immediate ancestor. This makes sense as both human and mouse "branches" on my phylogram are zero-length, and they are 99.7% identical in sequence. However, there are other zero-length branches. It seems that this is frowned upon? I tried to use other models to construct the tree, and still see the same result.
Is a phylogram like this not usable? I have used MEGA7 quite a lot before to make phylogenetic trees from comparative genomic analyses, and this is the first time that I am seeing this.
Any input will be greatly appreciated!