title: Bio++: efficient extensible libraries and tools for computational molecular evolution.
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.
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, CNRS, INRIA, Villeurbanne, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Guéguen
authors.forename: Sylvain
authors.initials: S
authors.lastname: Gaillard
authors.forename: Bastien
authors.initials: B
authors.lastname: Boussau
authors.forename: Manolo
authors.initials: M
authors.lastname: Gouy
authors.forename: Mathieu
authors.initials: M
authors.lastname: Groussin
authors.forename: Nicolas C
authors.initials: NC
authors.lastname: Rochette
authors.forename: Thomas
authors.initials: T
authors.lastname: Bigot
authors.forename: David
authors.initials: D
authors.lastname: Fournier
authors.forename: Fanny
authors.initials: F
authors.lastname: Pouyet
authors.forename: Vincent
authors.initials: V
authors.lastname: Cahais
authors.forename: Aurélien
authors.initials: A
authors.lastname: Bernard
authors.forename: Céline
authors.initials: C
authors.lastname: Scornavacca
authors.forename: Benoît
authors.initials: B
authors.lastname: Nabholz
authors.forename: Annabelle
authors.initials: A
authors.lastname: Haudry
authors.forename: Loïc
authors.initials: L
authors.lastname: Dachary
authors.forename: Nicolas
authors.initials: N
authors.lastname: Galtier
authors.forename: Khalid
authors.initials: K
authors.lastname: Belkhir
authors.forename: Julien Y
authors.initials: JY
authors.lastname: Dutheil
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods; D006801:Humans; D020407:Internet; D012984:Software
keywords: C++ libraries; bioinformatics; models of sequence evolution; phylogeny