Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.
Bioinformatics. 2010 Jun 15;26(12):i124-31. doi: 10.1093/bioinformatics/btq202.
Phylogenetic trees are widely used to display estimates of how groups of species are evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees are obtained for several datasets (e.g. for different genes), then their clusters are often contradicting. Consequently, the set of all clusters of such a dataset cannot be combined into a single phylogenetic tree. Phylogenetic networks are a generalization of phylogenetic trees that can be used to display more complex evolutionary histories, including reticulate events, such as hybridizations, recombinations and horizontal gene transfers. Here, we present the new Cass algorithm that can combine any set of clusters into a phylogenetic network. We show that the networks constructed by Cass are usually simpler than networks constructed by other available methods. Moreover, we show that Cass is guaranteed to produce a network with at most two reticulations per biconnected component, whenever such a network exists. We have implemented Cass and integrated it into the freely available Dendroscope software.
Supplementary data are available at Bioinformatics online.
系统发育树被广泛用于显示物种群体进化的估计。每棵系统发育树都可以看作是一簇簇的集合，是从共同祖先进化而来的物种的子群。当为几个数据集（例如不同的基因）获得系统发育树时，它们的聚类往往会相互矛盾。因此，这样的数据集的所有聚类的集合不能组合成一棵单个的系统发育树。系统发育网络是系统发育树的推广，可用于显示更复杂的进化历史，包括网状事件，如杂交、重组和水平基因转移。在这里，我们提出了新的 Cass 算法，该算法可以将任何一组聚类组合成一个系统发育网络。我们表明，Cass 构建的网络通常比其他可用方法构建的网络更简单。此外，我们表明，只要存在这样的网络，Cass 就保证在每个双连通分量中产生最多两个网状结构。我们已经实现了 Cass，并将其集成到免费提供的 Dendroscope 软件中。
补充数据可在“Bioinformatics”在线获取。
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