New version, new website!

The next release of the Bio++ libraries, version 3.00 is on its way. It includes major changes bringing even more flexibility for modeling sequence evolution. On this occasion, the website and documentation is being reorganized.

…

The Bio++ Project

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

An overview of the libraries and the underlying methods implemented is available on the Bio++ Wiki, as well as installation instructions.

API documentation

Detailed documentation of the classes can be found here:

• bpp-core
• bpp-seq
• bpp-phyl
• bpp-popgen
• bpp-seq-omics
• bpp-phyl-omics
• bpp-qt

Projects using the Bio++ libraries

• The Bio++ Program Suite provides a set of ready-to-use programs, allowing notably to process sequences, fit a large set of models of sequence evolution, or conduct population genetic analyses.

• TestNH provides some tools to fit complex non-homogeneous models, but also to perform substitution mapping.

• Grapes is a tool to fit models of distributions of fitness effects on polymorphism data and estimate the rate of adaptive non-synonymous substitutions.

• PhySamp provides programs to filter sequence alignments and phylogenies based on data availability and sequence similarity.

• CoMap is a package for the analysis of molecular coevolution.

• MafFilter is a genome alignment processor, allowing advanced filtering, format conversion and population genomic analyses.

Container

An apptainer recipe is available there:

• apptainer

as well as a debian computed image:

• debian