The R package ape, now in its fifth version, has evolved significantly over the past fifteen years, becoming a key tool for evolutionary biology research. Version 5.0 represents a major leap forward, offering improved efficiency, flexibility, and support for large datasets. It includes enhanced functions for handling phylogenetic trees and networks, such as reading trees with nodes of degree two and phylogenetic networks from extended Newick format files. The package now supports very long DNA sequences and phylogenies, with a limit of approximately 4.4 petabases for sequences and 4.4×10^15 sequences each of 4.4 petabases. ape also integrates with BioConductor and provides functions for reading FASTQ files, aiding in high-throughput sequencing data analysis. The package is available through CRAN and has been widely used, with over 22,000 downloads in a short period and over 600 citations in scientific journals. ape 5.0 improves performance by utilizing parallel computing and C++ code, enhancing the speed of data processing. It also includes functions to manage and compare phylogenetic trees, allowing users to compare trees based on their clades or bipartitions. Additionally, functions for managing labels in datasets have been improved, enabling more efficient data manipulation and analysis. The package continues to evolve to meet the growing demands of genomic data analysis, offering tools for handling large-scale data and supporting the study of biodiversity and evolution. The authors acknowledge the contributions of users and reviewers, and note that no conflicts of interest exist.The R package ape, now in its fifth version, has evolved significantly over the past fifteen years, becoming a key tool for evolutionary biology research. Version 5.0 represents a major leap forward, offering improved efficiency, flexibility, and support for large datasets. It includes enhanced functions for handling phylogenetic trees and networks, such as reading trees with nodes of degree two and phylogenetic networks from extended Newick format files. The package now supports very long DNA sequences and phylogenies, with a limit of approximately 4.4 petabases for sequences and 4.4×10^15 sequences each of 4.4 petabases. ape also integrates with BioConductor and provides functions for reading FASTQ files, aiding in high-throughput sequencing data analysis. The package is available through CRAN and has been widely used, with over 22,000 downloads in a short period and over 600 citations in scientific journals. ape 5.0 improves performance by utilizing parallel computing and C++ code, enhancing the speed of data processing. It also includes functions to manage and compare phylogenetic trees, allowing users to compare trees based on their clades or bipartitions. Additionally, functions for managing labels in datasets have been improved, enabling more efficient data manipulation and analysis. The package continues to evolve to meet the growing demands of genomic data analysis, offering tools for handling large-scale data and supporting the study of biodiversity and evolution. The authors acknowledge the contributions of users and reviewers, and note that no conflicts of interest exist.