Polyprotein phylogeny: substitution rate matrix

Question

[Sebastian L]

Hi everyone,

Please excuse me if the question is trivial, but i wasn't able to find any clear answer for this question anywhere yet...

I'm aligning amino-acid sequences which are part of a virus polyprotein (spans end of gene 1 and beginning of gene 2), which means all genes are translated during the same process and with the same mechanism (proteins are cleaved after translation).

I wonder if I can create a ML phylogenetic tree using with my whole sequence (i.e. 1 substitution rate matrix for both genes) or if I should create one tree per gene fragment even if they are translated as a polyprotein.

Thank you very much for your help!