TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core...

Area of Science:

• Bioinformatics
• Computational Biology
• Evolutionary Biology

Background:

• TOPALi v2 is a software package designed for evolutionary analysis.
• It offers a simplified and automated approach to complex bioinformatics tasks.
• The software is freely downloadable for major operating systems.

Purpose of the Study:

• To provide an integrated platform for evolutionary analysis of multiple sequence alignments.
• To automate and simplify the application of various phylogenetic and recombination detection methods.
• To facilitate accurate model selection and phylogenetic tree estimation.

Main Methods:

• Utilizes a Java graphical user interface for job submission.
• Employs TOPALi web services for remote or local execution on high-performance computing clusters.
• Integrates multiple phylogenetic inference methods, including Bayesian inference and Maximum Likelihood (ML).
• Incorporates accurate statistical criteria for optimal substitution model selection for diverse data types.
• Includes recombination detection methods.

Main Results:

• TOPALi v2 successfully automates and integrates multiple evolutionary analysis methods.
• The software facilitates accurate model selection and phylogenetic tree estimation.
• It supports both protein and nucleic acid data, including codon models.
• Phylogenetic software such as PhyML, RAxML, and MrBayes are integrated.

Conclusions:

• TOPALi v2 enhances the usability and efficiency of evolutionary sequence analysis.
• The platform simplifies complex computational tasks for researchers in evolutionary biology and bioinformatics.
• It provides a robust tool for phylogenetic inference and model selection.