I created a phylogenetic tree of several closely related ASVs and included a few reference strains. I'm seeing a really odd, long branch length on one of the sequences. Most of the branches are 0.01-0.04, and this one branch is 0.6. It is not in a distinct node. Is this likely due to an error? I aligned the sequences with MUSCLE and created the ML tree in MEGA. All of these sequences (including references) are highly similar to each other; they should be >95% identity. Should I use a different alignment tool and/or tree builder?
Even a small region of misalignment can do this. You always need to look at the alignment using a multiple sequence alignment viewer/editor. Aliview for Mac or BioEdit for Windows are both freeware.
You may need to check the coverage of your sequnces, in case of building a tree all sequences are better to have same length for better results.
Hi Teresa. Did you check if the weird sequence is in the right orientation? i.e. maybe you need to reverse-complement it. Good luck!
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