Hello, I am doing a project to implement the clustalW algorithm in an ARM processor, and although I understand the steps:

1. pairwise alignment
2. Construct the distance matrix
3. build the guide tree
4. Align the closest sequences or profiles.

My problem is that I do not understand in step 4 how these alignments are made. the only thing I know is that the PSW matrix is used.

My questions are : 1- With what alignment algorithms can the sequence-profile and profile-profile alignment (HMM or other) be used? 2. Is it valid for the ClustalW algorithm to make a consensus between sequences to solve the problem?

Sorry for the inconvenience, from step 4 I didn't actually find any information.