Hello to everyone :)
I need to build a HMM profile with hmmer without an MSA, i.e., I have a set of protein sequences that align in couples but I don't have the multiple sequence alignment. As far as I understood, with hmmer suite you can create an hmmer profile from a msa or a msa from a hmmer profile. Since I have none of these, is there a way to build an msa alignment in hmmer without the profile? I would like to avoid the use of other programs.
Everything I could find about this situation is a slide from a "Tandy Warnow" lecture that says
Profile HMMs can be built from a given multiple sequence alignment – this is not too difficult. Profile HMMs can also be built from unaligned sequences. This is a bit complicated.
And no further explanation.
Am I missing something?