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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
