Bioperl 1.5.2 review

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Bioperl project is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications

License: Artistic License
File size: 5717K
Developer: Bioperl developers
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Bioperl project is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS).

On the other hand, bioperl does provide reusable perl modules that facilitate writing perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.

In order to take advantage of bioperl, the user needs a basic understanding of the perl programming language including an understanding of how to use perl references, modules, objects and methods. If these concepts are unfamiliar the user is referred to any of the various introductory or intermediate books on perl.

We've liked S. Holzmer's Perl Core Language, Coriolis Technology Press, for example. This tutorial is not intended to teach the fundamentals of perl to those with little or no experience in the perl language. On the other hand, advanced knowledge of perl - such as how to write a object-oriented perl module - is not required for successfully using bioperl.

Bioperl is open source software that is still under active development. The advantages of open source software are well known. They include the ability to freely examine and modify source code and exemption from software licensing fees.

However, since open source software is typically developed by a large number of volunteer programmers, the resulting code is often not as clearly organized and its user interface not as standardized as in a mature commercial product.

In addition, in any project under active development, documentation may not keep up with the development of new features. Consequently the learning curve for actively developed, open source source software is sometimes steep.

What's New in This Release:
Many bugfixes and enhancements were made, including support for parsing the latest NCBI BLAST text format changes, PAML 3.15 support, a Taxonomy (Bio::Species) overhaul, a Bio::Map overhaul, a Bio::SearchIO speedup, the introduction of a Build.PL installation system, and fixes for some memory leaks in Bio::Tree.
This version requires Perl 5.6.1 or later.

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