The R package *ape* (Analyses of Phylogenetics and Evolution) has evolved significantly since its initial release in 2002, with version 5.0 marking a major advancement in modern phylogenetic and evolutionary analyses. This release focuses on improving efficiency, flexibility, and support for large datasets, particularly through the use of R's long vectors. Key enhancements include the ability to read trees with nodes of degree two and phylogenetic networks from extended Newick format files. The package now supports sequences longer than 2.1 Gb and can handle up to ≈4.4 Pb, far exceeding current genomic data sizes. Additionally, *ape* introduces functions for reading FASTQ files and parallel computing, enhancing data handling and analysis speed. New features also include improved data file management and label handling, making it easier for users to manage and compare phylogenetic trees and sequences. These improvements aim to make *ape* a versatile and efficient tool for biodiversity and evolutionary studies in the context of increasing data volumes.The R package *ape* (Analyses of Phylogenetics and Evolution) has evolved significantly since its initial release in 2002, with version 5.0 marking a major advancement in modern phylogenetic and evolutionary analyses. This release focuses on improving efficiency, flexibility, and support for large datasets, particularly through the use of R's long vectors. Key enhancements include the ability to read trees with nodes of degree two and phylogenetic networks from extended Newick format files. The package now supports sequences longer than 2.1 Gb and can handle up to ≈4.4 Pb, far exceeding current genomic data sizes. Additionally, *ape* introduces functions for reading FASTQ files and parallel computing, enhancing data handling and analysis speed. New features also include improved data file management and label handling, making it easier for users to manage and compare phylogenetic trees and sequences. These improvements aim to make *ape* a versatile and efficient tool for biodiversity and evolutionary studies in the context of increasing data volumes.