PhyloNetworks: A Package for Phylogenetic Networks.

Area of Science:

• Computational Biology
• Evolutionary Biology
• Bioinformatics

Background:

• Phylogenetic networks are crucial for understanding complex evolutionary histories, including hybridization and horizontal gene transfer.
• Existing software often lacks comprehensive tools for inferring, visualizing, and analyzing these complex evolutionary structures.
• There is a need for integrated software that supports advanced phylogenetic network analyses.

Purpose of the Study:

• To introduce PhyloNetworks, a novel Julia package for phylogenetic network inference, manipulation, and analysis.
• To provide tools for summarizing sets of phylogenetic networks and assessing support for evolutionary relationships.
• To enable phylogenetic comparative analyses using phylogenetic networks.

Main Methods:

• Phylogenetic network inference using maximum pseudolikelihood from gene trees or multi-locus sequences (SNaQ).
• Bootstrap analysis for assessing the robustness of inferred phylogenetic networks.
• Development of novel methods for summarizing network ensembles and quantifying support for hybrid edges and nodes.

Main Results:

• PhyloNetworks offers a comprehensive environment for interactive phylogenetic network analysis.
• The package provides the first tools to summarize sets of networks, including measures of tree, hybrid edge, and hybrid node support.
• Phylogenetic networks generated by PhyloNetworks can be directly used for phylogenetic comparative analyses.

Conclusions:

• PhyloNetworks is a powerful and versatile open-source software package for advancing phylogenetic network research.
• The software facilitates robust inference and comprehensive analysis of complex evolutionary histories.
• PhyloNetworks enhances the application of phylogenetic networks in evolutionary biology and comparative genomics.