You could run a model test to see what substitution profile best suits your data. In my opinion, the easiest way to do that currently is using IQtree ( http://www.iqtree.org/doc/Substitution-Models ), as it returns understandable output when model testing. Their documentation also provides useful summaries of what particular models are suitable for.

Keep in mind that the quality and quantity of your data guides that process. You can then apply the suggested model in RaxML, and compare against IQTree inference.

Also, if I understand you correctly you are inferring a tree from a single tree. Keep in mind that the resulting tree, if resolved, traces the evolution of that gene, which may or may not correlate to species phylogeny.

Hope that helps :)