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Updated: Jun 30, 2026
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs
Julien Dutheil1, Bastien Boussau
1BiRC - Bioinformatics Research Center, University of Aarhus, C, F, Møllers Alle, DK-8000 Arhus C, Denmark. jdutheil@daimi.au.dk
BMC Evolutionary Biology
|September 24, 2008
Summary
This study introduces a flexible Bio++ library for non-homogeneous sequence evolution models, enabling accurate phylogenetic analysis and realistic data simulation. The new tools facilitate advanced evolutionary modeling and parametric bootstrapping for robust biological research.
Area of Science:
- Computational Biology
- Evolutionary Biology
- Bioinformatics
Background:
- Accurate modeling of sequence substitution is crucial for estimating evolutionary parameters like phylogenetic relationships and substitution rates.
- Homologous sequences often exhibit varying compositions, necessitating non-homogeneous models to capture lineage-specific evolutionary changes.
- Existing non-homogeneous models have limitations in flexibility and data simulation capabilities.
Purpose of the Study:
- To present a general implementation of non-homogeneous models for sequence evolution within the Bio++ libraries.
- To introduce user-friendly programs for parameter estimation and sequence data generation using these models.
- To provide a flexible and efficient framework for advanced evolutionary analyses.
Main Methods:
- Developed dedicated classes for non-homogeneous substitution models in C++.
- Created Bio++ Maximum Likelihood (BppML) for parameter estimation.
- Developed Bio++ Sequence Generator (BppSeqGen) for simulating sequence evolution.
- Implemented a property file syntax for defining non-homogeneous models without programming.
Main Results:
- A general implementation of non-homogeneous models is now available in the Bio++ libraries.
- BppML and BppSeqGen enable parameter estimation and sequence simulation for a wide range of non-homogeneous models.
- The property file syntax allows for easy model description and customization.
Conclusions:
- The general implementation accommodates diverse non-homogeneous models, including heterotachous ones, with computational efficiency.
- The developed tools support parametric bootstrapping and non-homogeneity testing.
- These advancements enhance the accuracy and scope of evolutionary sequence analysis.
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