Bio++: efficient, extensible libraries and tools for computational molecular evolution

Efficient algorithms and programs for the analysis of the ever-growing amount of biological sequence data are strongly needed in the genomics era. The pace at which new data and methodologies are generated calls for the use of pre-existing, optimized – yet extensible – code, typically distributed as libraries or packages. This motivated the Bio++ project, aiming at developing a set of C++ libraries for sequence analysis, phylogenetics, population genetics and molecular evolution. The main attractiveness of Bio++ is the extensibility and reusability of its components through its object-oriented design, without compromising on the computer-efficiency of the underlying methods. We present here the second major release of the libraries, which provides an extended set of classes and methods. These extensions notably provide built-in access to sequence databases and new data structures for handling and manipulating sequences from the omics era, such as multiple genome alignments and sequencing reads libraries. More complex models of sequence evolution, such as mixture models and generic n-tuples alphabets, are also included.
The article was published May 21st, 2013. Read the full article : Bio++: efficient, extensible libraries and tools for computational molecular evolution

Bio++ packaging

What does it take for Bio++ to enter the official repositories of Debian GNU/Linux ?

Request For Packaging

The first step is to ask for a Debian Developer to package the software. This is called a RFP as in Request For Packaging and it is done by filling a bug report against the wnpp pseudo package. Since Debian packages for Bio++ are already provided the task of the Debian Developer is facilitated.
Even when Debian packages are already available, the odds of seducing a Debian Developer into taking responsibility for the package are small. The quality standards for a package entering Debian are higher than what is implemented by the amateur packager. However, meeting these standards is not a difficult task when using the proper tools.

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