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Updated: Apr 28, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.

Filip Bielejec¹, Philippe Lemey, Luiz Max Carvalho

¹Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium. filip.bielejec@rega.kuleuven.be.

BMC Bioinformatics

|June 3, 2014

Summary

This summary is machine-generated.

We developed πBUSS, a flexible tool for simulating molecular sequences under complex evolutionary models. This aids in assessing phylogenetic reconstruction methods and enhances evolutionary inference studies.

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Published on: August 14, 2018

Area of Science:

Computational Biology
Evolutionary Biology
Bioinformatics

Background:

Phylogenetic reconstruction methods rely on simulated sequences for performance assessment.
BEAST is a Bayesian framework for time-calibrated molecular evolution but lacks simulation tools.
Existing tools do not adequately support complex evolutionary models for simulation.

Purpose of the Study:

To introduce πBUSS, a novel Monte Carlo simulation tool for phylogenetic analyses.
To provide a flexible and user-friendly platform for generating sequence alignments under diverse evolutionary models.
To enhance the capabilities of phylogenetic inference tools like BEAST.

Main Methods:

Utilizes the BEAGLE high-performance library for rapid sequence alignment generation.
Features a graphical user interface (GUI) and a command-line interface for flexible model application.
Integrates with BEAST by parsing common extensible markup language (XML) formats for advanced models.

Main Results:

πBUSS enables rapid generation of large sequence alignments using complex evolutionary models.
The tool offers a rich array of models applicable across multiple partitions.
Facilitates large-scale simulation studies through scripting and a user-friendly GUI.

Conclusions:

πBUSS provides a flexible and easy-to-use solution for sequence simulation under realistic evolutionary scenarios.
Supports simulation studies from basic illustration to complex performance assessments.
Applicable beyond the BEAST framework, connecting with other programs via standard I/O.