Multiple Sequence Alignment using Hidden Markov Model (HMM)

Hi, I am currently trying to get 2 pdb files and perform a sequence alignment between them with the use of hmm algorithm.

Currently I am using the 'getpdb' function to get the residue and from there can obtain the sequence.

I know there are HMM functions that exist but either I do not know how to implement them correctly or they do not work in the way I imagine them to run.

I am comparing the nwalign algorithm with hmm.

Any feedback will be greatly appreciated.

Kind regards,

Tanil Patel