What Is A Substitutionmatrix Used For?

Question

[loicatraile]

Hi biostars! I know that substitution matrices are used to reconstruct evolutionary trees. My question is what roll do they play in the reconstruction (how does it work)? and what are the results in the reconstruction if you use a different matrix? you get another tree?

thanks for the reply!

Answer 1

[lkmklsmn]

Substitution matrices are used to quantify the 'difference' between amino acids or nucleotides between species. For example BLOSUM. For biochemical reasons, a change from His to Glu is not as 'bad' as a change from Glu to Cys. Based on these scores you can then calculate a phylogenetic distance between species. So to answer your questions, the substitution matrix may change your tree depending on your data. Generally however, these changes are details, which may or may not be important.