Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph.
Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph.
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DOI：
10.1007/s00285-023-02006-3
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发表时间：
2023-10-25
影响因子：
1.9
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中科院分区：
文献类型：
--
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在许多情况下，不仅要知道给定数据集的最佳系统发育树，而且要知道高质量树的集合。这一目标通常使用贝叶斯技术来解决，然而，当前的贝叶斯方法不能扩展到大型数据集。此外，对于具有相对低信号的大数据集，甚至不能单独存储每棵好树，特别是当树需要分叉时。在本文中，我们开发了一种新的对象称为“历史子分区有向无环图”（或简称“历史SDAG”），companion表示一个合奏的标签（例如祖先序列）映射到内部节点的树。历史sDAG可以被有效地构建，并且也可以被有效地修剪以仅表示最大简约树。我们表明，历史SDAG允许我们找到许多额外的同样简约的树，扩展组合超出用于构建it.We的合奏认为，这个对象可能是有用的“骨架”的一个更完整的不确定性量化。
In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but the collection of high-quality trees. This goal is typically addressed using Bayesian techniques, however, current Bayesian methods do not scale to large data sets. Furthermore, for large data sets with relatively low signal one cannot even store every good tree individually, especially when the trees are required to be bifurcating. In this paper, we develop a novel object called the “history subpartition directed acyclic graph” (or “history sDAG” for short) that compactly represents an ensemble of trees with labels (e.g. ancestral sequences) mapped onto the internal nodes. The history sDAG can be built efficiently and can also be efficiently trimmed to only represent maximally parsimonious trees. We show that the history sDAG allows us to find many additional equally parsimonious trees, extending combinatorially beyond the ensemble used to construct it. We argue that this object could be useful as the “skeleton” of a more complete uncertainty quantification.
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