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. 2018 Mar 15;34(6):1056-1057.
doi: 10.1093/bioinformatics/btx740.

SPECTRE: a suite of phylogenetic tools for reticulate evolution

Sarah Bastkowski  1 , Daniel Mapleson  1 , Andreas Spillner  2 , Taoyang Wu  3 , Monika Balvociute  4 , Vincent Moulton  3
Affiliations

SPECTRE: a suite of phylogenetic tools for reticulate evolution

Sarah Bastkowski et al. Bioinformatics. .

Abstract

Summary: 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.

Availability and implementation: 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/.

Contact: sarah.bastkowski@earlham.ac.uk.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1
Fig. 1
To illustrate some of SPECTREs functionality, we processed a dataset analyzed in (Bollyky et al., 1996) consisting of different Hepatitis B viruses (HBV). There are five different genomic groups and the phylogenetic analysis led to the result that HBVDNA is a recombinant with around half the genome coming from group A and half from group D. It also concluded that HPBADW1 is a recombinant of HPBADW2 (B) and HPBADWZCG (A), but with only a small insertion from HPBADWZCG into the Genome. (a) A minimum evolution tree constructed by NetME that is compatible with the split network constructed by NeighborNet, which is shown in (b). (c) The split network constructed by FlatNJ
See this image and copyright information in PMC

References

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    1. Bollyky P.L. et al. (1996) Recombination between sequences of hepatitis B virus from different genotypes. J. Mol. Evol., 42, 97–102. - PubMed
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