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