DNA Subway or MEGA

Question

[sushi]

Which generates a more reliable data?

I used both platforms for alignment and construction of phylogenetic tree for trnL-trnF sequences. I find DNA Subway easier to use because it helps me to automatically trim gaps. In addition, I was able to generate rooted tree here. However, I am unable to find supporting journals for this.

MEGA

I used MUSCLE algorithm and UPGMA clustering method for alignment, while I did not trim gaps and construct NJ tree here.

DNA Subway

I hope you can help me with this. Thank you very much!