SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution

ABSTRACTSummarySplit-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks, including split-decomposition, NeighborNet, QNet and FlatNJ. Some of these approaches are implemented in the user-friendly SplitsTree software package. However, to give the user the option to adjust and extend these approaches and to facilitate their integration into analysis pipelines, there is a need for robust, open-source implementations of associated data structures and algorithms. Here we present SPECTRE, a readily available, open-source library of data structures written in Java, that comes complete with new implementations of several pre-published algorithms and a basic interactive graphical interface for visualizing planar split networks. SPECTRE also supports the use of longer running algorithms by providing command line interfaces, which can be executed on servers or in High Performance Computing (HPC) environments.AvailabilityFull source code is available under the GPLv3 license at: https://github.com/maplesond/SPECTRESPECTRE’s core library is available from Maven Central at: https://mvnrepository.com/artifactuk.ac.uea.cmp.spectre/coreDocumentation is available at: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/[email protected] Information (SI)Supplementary information is available at Bioinformatics online.

QUARTETS AND UNROOTED PHYLOGENETIC NETWORKS

Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data. In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analog of level-k networks. In particular, we give an equivalence theorem between circular split systems and unrooted level-1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted level-k phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions.