Comparing two HMM profiles

Question

[kk1990]

Hi!

I have several HMM profiles of proteins generated from alignments using hmmbuild from hmmer package. How can I compare each vs. each?

Thank you in advance

Answer 1

[Jean-Karim Heriche]

The Kullback-Leibler distance has often been used to compare HMMs but there are a number of other measures e.g. this paper or this one.