[Biojava-l] Multiple sequence alignment in BioJava

[Alastair Kilpatrick]

Dear all,
I'm pretty new to BioJava so I may be missing something - I've checked
through the list archives without much luck.
I've been trying to do some multiple sequence alignments but I've been
running into strange errors. To try and find where the problem is,
I've just copied the code straight from
http://biojava.org/wiki/BioJava:CookBook3:MSA and tried to run it, but
I'm still getting an error:

Caused by: java.lang.ClassNotFoundException:
org.forester.phylogenyinference.DistanceMatrix

It would seem that this is something to do with forester.jar, which I
had to download separately (from http://code.google.com/p/forester/)
as per http://biojava.org/wiki/BioJava:CookBook#biojava3-alignment -
when I look through the jar in Eclipse, there isn't anything named
'phylogenyinference', although there is 'phylogeny', 'phylogeny.data',
'phylogeny.factories' and 'phylogeny.iterators'. Is there something
I'm doing wrong, or is it the case that either one of BioJava or
forester has been updated and things have broken somewhere (I see the
CookBook page was updated in July 2010 but forester was updated just
last month)? Either way, any ideas would be much appreciated!

Many thanks,
Alastair Kilpatrick

PhD candidate,
School of Informatics, University of Edinburgh