As reported via e-mail, the current code of Builder.build_msa was not producing HMMs consistent with hmmbuild.
The issue was occurring because the builder was always using gap-open and gap-extend probabilities to compute the transition probabilities instead of the alignment itself.
As reported via e-mail, the current code of
Builder.build_msawas not producing HMMs consistent withhmmbuild.The issue was occurring because the builder was always using gap-open and gap-extend probabilities to compute the transition probabilities instead of the alignment itself.