I am new to research. As part of my MRes, I am required to create a phylogenetic tree(s) of my genes of interest. I am currently blasting (tblastn) my genes of interest from S. mediterranea against model systems before expanding my search.
Problem is, I get something like the attached which does not look like right. What am I doing wrong? I'm alinging using MUSCLE, and running Maximum Likliehood Protein models and consequentially, using the correct model (JTT, for instance).
Greatly appreciate any help in advance.