SPECTRE: a suite of phylogenetic tools for reticulate evolution

Split-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 environments. Full source code is available under the GPLv3 license at: https://github.com/maplesond/SPECTRE. SPECTRE’s core library is available from Maven Central at: https://mvnrepository.com/artifact/uk.ac.uea.cmp.spectre/core. Documentation is available at: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/ Supplementary data are available at Bioinformatics online.

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Author Bastkowski, Sarah
Last Updated November 20, 2019, 16:44 (UTC)
Created August 1, 2019, 10:29 (UTC)
Article Host Type publisher
Article Is Open Access true
Article License Type cc-by
Article Version Type publishedVersion
Citation Report https://scite.ai/reports/10.1093/bioinformatics/btx740
DOI 10.1093/bioinformatics/btx740
Date Last Updated 2019-06-04T14:34:49.706712
Evidence open (via page says license)
Funder code(s)
Journal Is Open Access false
Open Access Status hybrid
PDF URL https://academic.oup.com/bioinformatics/article-pdf/34/6/1056/25119396/btx740.pdf
Publisher URL https://doi.org/10.1093/bioinformatics/btx740