bioperl reviews

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BioPerl (1.007002) *****

BioPerl is the standard library for bioinformatics in Perl. Its design leans fairly heavily on concepts borrowed from Java and other object-oriented languages (for example, the separation between interfaces and implementation classes), which means that it is somewhat hard to understand the sprawling architecture at first but also that it is very, very extensible.

Once you get it - and there is good documentation and a user community to help you with this - it turns out to be very useful. This is probably especially true for the many different file readers and writers. Bioinformatics is unfortunately plagued by a proliferation of file formats, many of which are represented in BioPerl. Other good things are the interfacing with web services and databases, and the architecture for invoking command line tools and parsing the results.

If you are doing something with biological data in Perl you probably need to learn BioPerl.

BioPerl (1.6.901) *****

I always seem to have install problems on OSX, but I think that is the nature of the beast. Overall, this package is fantastic :)

bioperl (1.5.2_RC4) **

Awkward interface, O(n^2) performance where you don't expect it... Try to roll your own before using this module.

bioperl (1.4) ***

Good news: bioperl is fairly complete and correct, as far as I can tell.

Bad news: it's absolute agony to use, making easy things hard, and hard things slow. A few points:
* The interface is a twisty little maze of objects, all alike.
* Many methods are unnecessarily slow.
* Some formats (e.g. BLAST) are incompletely supported.
* The documentation "follows standards", which means that many of the less-used bits are documented with a pile of uninformative but mandatory boilerplate.
* For simple tasks, it's usually easier to roll your own than to wade through the docs.

Other modules are a better bet if they meet your needs -- see e.g. Chemistry::* and Boulder::* .

bioperl (1.4) *****

*The* bundle if you have something to do with bioinformatics. Only thing i feel pitty is that most functionality would have been better a standalone module. Because not everything BIO only in there.
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