Since Darwin, phylogenetic trees have been widely used to represent the evolutionary history of species and other taxonomic groups. In cases where reticulate evolutionary events, such as horizontal gene transfer, speciation by hybridization or reassortment, play a notable role, phylogenetic networks are sometimes employed. Here, we present the SplitsTree App, which is software for exploring and analyzing phylogenetic data using both trees and networks. Offering a comprehensive set of features, the application provides over 100 algorithms for computing distances, phylogenetic trees, split networks, haplotype networks, rooted phylogenetic networks, tanglegrams, consensus trees and consensus networks. It introduces a faster version of neighbor-net1 and provides an implementation of median-joining, which are the two most widely used techniques for constructing phylogenetic networks. Moreover, the software incorporates genetic and phylogenetic indices, ranging from Tajima’s D for sequences to Shapely values on phylogenetic networks. A complete description of all the program’s features can be found in the Supplementary User Manual.This new software is designed to accommodate the increasing scale and intricacy of modern datasets. It extends, integrates and supersedes our earlier applications SplitsTree4 (ref. 2) for unrooted phylogenetic trees and networks, Dendroscope3 (ref. 3) for rooted trees and networks, and PopArt4 for haplotype analysis. Unrooted networks are widely used in phylogenetics and population genetics5,6, but also in other fields such as linguistics and anthropology7. While rooted phylogenetic networks have the potential to explicitly represent reticulate evolution8, they have faced limited adoption because of a lack of applicable software. To address this, the SplitsTree App provides new methods for computing these networks9.
