In Which Order Would a Molecular Evolutionist Perform the Following $\rightarrow$

In which order would a molecular evolutionist perform the following tasks: (1) construct a similarity matrix, (2) align the sequences, and (3) use a model of evolution to correct for multiple substitutions and other factors?

A) 1 $\rightarrow$ 2 $\rightarrow$ 3
B) 1 $\rightarrow$ 3 $\rightarrow$ 2
C) 2 $\rightarrow$ 1 $\rightarrow$ 3
D) 2 $\rightarrow$ 3 $\rightarrow$ 1
E) 3 $\rightarrow$ 2 $\rightarrow$ 1