[Biojava-l] Algorithm to compare protein sequences

[Andreas Dräger]

Hi Mara,

At the moment there are two alignment algorithms available:
Smith-Waterman for local and Needleman-Wunsh for global alignment. In
addition to that there is a package for hidden Markov models that is
also able to perform sequence alignments (see the BioJava cookbook for
examples). However, currently both approaches will write the alignment
similar to the BLAST output and not in this Newick format (I am actually
not familiar with that). I hope that helps.

Cheers
Andreas

-- 
Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 Tübingen
Germany

Phone: +49-7071-29-70436
Fax:   +49-7071-29-5091