Excellent answers given above.
For a little light relief, see:
www.tapetum.com; follow the BioFractal link.
danielh at tapetum dot com
George Armhold wrote:
>> I am interested in hearing of any freely-available Java
> implementations of software for molecular biology. There is certainly
> no dearth of Perl implementations, but I have seen very little done in
> Java. If you have written or have access to some code you would like
> to share, please drop me a note. Depending on the response I get, I
> am considering setting up some sort of repository similar to what they
> have done on http://bio.perl.org.>> A few words about my motivation. I am a programmer relatively new to
> the field of Bioinformatics. I've certainly written my share of Perl
> code, and recognize its value. At the present time, nothing can beat
> Perl when it comes to parsing text, which is a task performed
> constantly in this field. However there are times when Perl is
> downright frustrating to use due to its lack of support for complex
> data structures. The text-parsing abilities of Java are gradually
> improving, and IMHO some applications would benefit from being written
> in Java, even considering the relatively poor state of its
> text-parsing code at the present moment compared to Perl.
> George Armhold PGP Key: [02D2EBE5]
> Rutgers University Fingerprint: [51 8B A4 B0 7A 71 7C E7]
> Bioinformatics Initiative [85 DE 13 99 0B 68 5F 92]