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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

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Published on: May 28, 2021

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

Laurent Guéguen1, Sylvain Gaillard, Bastien Boussau

  • 1Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, CNRS, INRIA, Villeurbanne, France.

Molecular Biology and Evolution
|May 24, 2013
PubMed
Summary
This summary is machine-generated.

The Bio++ project offers extensible C++ libraries for analyzing biological sequence data in genomics. This second release enhances capabilities with database access and new structures for omics data analysis and evolutionary models.

Keywords:
C++ librariesbioinformaticsmodels of sequence evolutionphylogeny

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The rapid growth of biological sequence data necessitates efficient and reusable computational tools.
  • Existing methodologies require optimized and extensible code, often distributed as software libraries.

Purpose of the Study:

  • To introduce the second major release of the Bio++ C++ libraries.
  • To provide enhanced functionalities for sequence analysis, phylogenetics, population genetics, and molecular evolution.

Main Methods:

  • Development of object-oriented C++ libraries for biological sequence analysis.
  • Implementation of extensible and reusable code components.
  • Integration of new data structures and access to sequence databases.

Main Results:

  • The Bio++ libraries now include built-in access to sequence databases.
  • New data structures support handling of omics-era sequences like multiple genome alignments and sequencing reads.
  • Advanced models for sequence evolution, including mixture models and generic n-tuples alphabets, are incorporated.

Conclusions:

  • The enhanced Bio++ libraries offer improved efficiency and extensibility for biological data analysis.
  • The new features facilitate the analysis of complex genomic and molecular evolution data.
  • Bio++ provides a robust framework for addressing challenges in the genomics era.