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

Item Type:Article
Title:Bio++: efficient extensible libraries and tools for computational molecular evolution
Creators Name:Gueguen, L. and Gaillard, S. and Boussau, B. and Gouy, M. and Groussin, M. and Rochette, N.C. and Bigot, T. and Fournier, D. and Pouyet, F. and Cahais, V. and Bernard, A. and Scornavacca, C. and Nabholz, B. and Haudry, A. and Dachary, L. and Galtier, N. and Belkhir, K. and Dutheil, J.Y.
Abstract: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 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.
Keywords:Bioinformatics, Models of Sequence Evolution, Phylogeny, C++ Libraries
Source:Molecular Biology and Evolution
ISSN:0737-4038
Publisher:Oxford University Press (U.S.A.)
Volume:30
Number:8
Page Range:1745-1750
Date:August 2013
Official Publication:https://doi.org/10.1093/molbev/mst097
PubMed:View item in PubMed

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