SPECTRE: a suite of phylogenetic tools for reticulate evolution

被引：8

作者：

Bastkowski, Sarah ^{[1
]}

Mapleson, Daniel ^{[1
]}

Spillner, Andreas ^{[2
]}

Wu, Taoyang ^{[3
]}

Balvociute, Monika ^{[4
]}

Moulton, Vincent ^{[3
]}

机构：

[1] Earlham Inst, Norwich Res Pk, Norwich NR4 7UZ, Norfolk, England

[2] Merseburg Univ Appl Sci, D-06217 Merseburg, Germany

[3] Univ East Anglia, Sch Comp Sci, Norwich NR4 7TJ, Norfolk, England

[4] Univ Tubingen, Dept Comp Sci, Sand 14, D-72076 Tubingen, Germany

来源：

BIOINFORMATICS | 2018年 / 34卷 / 06期

关键词：

AGGLOMERATIVE METHOD; NETWORKS; CONSTRUCTION; QUARTETS;

D O I：

10.1093/bioinformatics/btx740

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1056 / 1057

页数：2