[Biojava-l] Compare Bioperl and Biojava Pls.

[Thomas Down]

On Thu, Feb 07, 2002 at 10:45:57AM -0800, Anu Padki wrote:
> Hi Gurus at Biojava,
> 
> I am trying to find out which one to go for, BioPerl or BioJava?

I'd just like to second Simon's comments on this: both these
packages (and BioPython, and BioRuby, for that matter) contain
a lot of useful code.  Unless there's some very specific
feature in one of the libraries which is definitely going
to save you a lot of time, I think you're better off making
a choice on the basis of which language you prefer, rather than
which library.

To a large extent, I think the designs of the various
bioinformatics libraries reflect the designs and philosophies
of their implementation languages.

> Can someone tell me why there was a need for BioJava ?

Beacuse people were writing bioinformatics software in Java,
and wanted to share core interfaces and components.

> How is it better/different from BioPerl?

In many areas, the differences are fairly peripheral, and
have as much to do with language differences as anything
else.

One area where there /is/ a big difference is that the
Sequence APIs in BioJava are designed to support sequence
analysis applications.  At the core, there is a strongly
abstract algebraic symbol/alphabet model.  There is also
a fairly sophisticated dynamic programming library included,
which is a good starting point for many types of analsis.

Bioperl's strengths lie more in the direction of launching
external tools to perform analyses (as might be expected,
given Perl's background).


I hope you find this helpful -- good luck with whichever
library you choose,

    Thomas.