[Biojava-l] nightly builds

Hello - Is there a plan to reinstate the nightly builds? Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 ___

[Biojava-l] Using pairwiseDP

Hi, I am trying to use BioJava for doing alignment between two sequences. I tried to use the pairwiseDP class, but it is not clear to me how to construct a MarkovModel for it. The problem, I think, is specifying the emission distributions for pair symbols with gaps. How can you create a pairDis