I want to study if matK could be a potential locus for identifying a certain plant genus. I aligned matK sequences using MEGA software with MUSCLE algorithm and UPGMA as its clustering method. After deciding not to trim any gaps, I proceeded with reconstructing NJ tree in MEGA as well.

I wonder if retaining the gaps is the reason why I got a low bootstrap value or is it due to the methods that I have use?

I hope you could help me with this as this is also my first time conducting this type of study.

Your tips is highly appreciated, thank you very much!