I made MSA of homologous protein sequences by muscle. Next after alignment trimming (removing MSA columns >50% gaps), I built phylogenetic tree by raxml with 1000 bootstraps and LG+I+G substitution model. I converted the MSA to codon alignment by pal2nal, and built the tree with GTR substitution model.
The resulting trees differ quite a bit. I am wondering which one is more reliable if it is proper to compare the trees. Let me know if there is any paper which compares these two scenarios.