I am trying to determine if a particular plant protein I am studying has sites of positive selection. Unfortunately, I only have sequences from 6 different species within the same family. I did a Muscle codon alignment of these sequences using MEGA and then used the REL algorithm with a cutoff of 50 on the Datamonkey website to determine selection at each site. The problem I am having is that every time I input the same exact alignment, Datamonkey keeps giving me a different answer. Is this because my alignment has two few sequences to generate a statistically significant result? Is there a better algorithm on Datamonkey I should be using?