SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution

Abstract

SummarySplit-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.\n\nAvailabilityFull source code is available under the GPLv3 license at: https://github.com/maplesond/SPECTRE\n\nSPECTREs core library is available from Maven Central at: https://mvnrepository.com/artifactuk.ac.uea.cmp.spectre/core\n\nDocumentation is available at: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/\n\nContactsarah.bastkowski@earlham.ac.uk\n\nSupplementary Information (SI)Supplementary information is available at Bioinformatics online.