It seems that HMMER2/3 is an integrated package in ugene and not listed as external tool. However the sample data did not work with it in ugene version 1.9.2. Is it possible for circumstances like this we call hmmer2/3 from somewhere in ugene?

HMMER 2/3 is integrated directly into UGENE, it's not an external tool.
What sample data did you use?

I used the sample data from

C:\Program Files\Unipro UGENE\data\samples\HMM\aligment15900.hmm

It stated hmmer 2. And there was no *.sto file.

I have since referred to HMMER3, download and use that example it works in building the profile and the search on local does one search at a time... can we make it take a fasta file with a few fasta file and search in just one run to get all the profile searches in one go?

Perhaps it is a good idea to provide test sample for each of the tools. In this case it needed an update.

Seriously do we still need hmmer2 since we have the faster hmmer3?

Thanks.

Can we output hmm format and not in gb so that we can parse it with other parsers?