How do we interpret the distance or percent identity output of Clustal Omega?
I run Clustal Omega on some selected sequences from a homologous cluster but it happens that the percent identity it returns between sequences can be around 30%, even 19%.
Does that mean these sequences should not even be in a homologous cluster? What is a good threshold on percent identity (produced by Clustal Omega) to tell two sequences are similar? What is the minimum identity that indicates a good match?