[Bioperl-l] domain aligned global protein multiple sequence alignment

[onlyIDleft]

Are there tools in BioPerl that will allow me to obtain multiple sequence
alignment of proteins but with a twist

All the proteins I deal with have at least one protein domain (as defined by
Pfam HMM models)

So I want to constrain this global multiple sequence alignment with the fact
that all domains should be aligned to one another....

I could do it iteratively by using HMM align in HMMER3 for each domain, and
then use this alignment as a constraint for the global alignment by T-COFFEE
or some such strategy.

But this is too manually intensive and cumbersome, are there BioPerl tricks
that can be used to achieve my goal?
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