PhyloProfile v2: Scalable Exploration of Multilayered Phylogenetic Profiles via Dimensionality Reduction

Abstract

Phylogenetic profiles - presence-absence patterns of genes across taxa - are rich information sources for inferring the evolutionary history of genes and gene families. When aggregated across many genes, these profiles can reveal coevolutionary patterns, supporting the prediction of gene functions and interactions. With rapidly growing numbers of sequenced genomes, phylogenetic profiles now routinely encompass thousands of genes and taxa. Existing software fall short in enabling interactive visualization, exploration, and analysis of such large datasets. We present PhyloProfile v2, a comprehensive overhaul of the original PhyloProfile software. This new version introduces major performance improvements along with novel features designed for more efficient data exploration. Notably, PhyloProfile v2 integrates dimensionality reduction techniques to visualize phylogenetic profiles in interactive 2D or 3D space, offering an intuitive overview even for massive datasets. Furthermore, the platform enables seamless transitions from large-scale analyses - spanning millions of orthology relationships - to detailed comparisons of protein feature architectures between specific orthologs. PhyloProfile v2 thus provides a versatile and scalable solution for evolutionary and functional genomics research. PhyloProfile v2 is available as an R package at Bioconductor https://doi.org/doi:10.18129/B9.bioc.PhyloProfile. The open-source code and documentation are provided under MIT license at https://github.com/BIONF/PhyloProfile