BioPerl reviews

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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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