Suppose, Protein X is a protozoan protein and it has more than one homolog in different species. Which method should I use to build up the phylogenetic tree by taking protein homolog from different model organisms or different species? I want to know how the protein sequence changes over evolution from lower to higher organisms and how can I group different homologs.
Your question is a bit confusing. What are you actually asking? Are you asking about the method of phylogenetic tree construction or asking for the choices of sequences/queries?
Nevertheless, "different model organisms or different species", its your choice. However, if you have only different species of your organism, how could you see what you want to see?
Another thing is, in case of functional proteins, one can not conclude about evolution without the descriptive synonymous vs non-synonymous substitution analysis.
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