Thank you for the great improvements that ugene has seen over the last couple of years.
I would like to suggest to include the software cd-hit (http://cd-hit.org) as a plugin. This would help to reduce the complexity of large datasets of homologous sequences by automatically selecting representative sequences which feature identities below a certain identity threshold. I would suggest to consider including the two basic functions of the cd-hit suite, cd-hit for protein sequences and cd-hit-est for DNA sequences (http://weizhongli-lab.org/cdhit_suite/cgi-bin/index.cgi).
Thank you for your consideration.