[Biojava-l] can BioJava do alignment ?

[Carmel Kent]

Hello,

I'm interested in a Java package for sequence alignment.
I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it can
only create objects that are representations of alignments generated by
third-party software.

I had an impression that      BioJava 1.5 can do alignment itself (e.g., I
saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
named org.biojava.bio.alignment.NeedlemanWunch)

I have two questions:

   is this true ? I mean, does BioJava 1.5 contain the alignment algorithm,
   itself ?
   if it does, I downloaded the CVS view of BioJava 1.5, but could not find
   any javadocs or the alignment package source. Where can I find it ?



Thanks very much,


Carmel Kent
Research Staff Member
Healthcare I/T Research
IBM Research Laboratory in Haifa
Tel. +972-4-8281059
Email: carmelk at il.ibm.com