A congruence index for testing topological similarity between trees
A congruence index for testing topological similarity between trees
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DOI：
10.1093/bioinformatics/btm500
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发表时间：
2007-12-01
期刊：
影响因子：
5.8
通讯作者：
Martin, Olivier C.
中科院分区：
文献类型：
--
作者：
de Vienne, Damien M.;Giraud, Tatiana;Martin, Olivier C.
动机：系统发生树在进化生物学中无处不在，树的比较在其中发挥着核心作用。树全等统计基于零假设，即两棵给定的树并不比偶然预期的更全等（拓扑相似）。通常，人们会搜索与两棵树相关的最简约的进化场景，然后通过生成大量随机树并将它们与观察到的树之间的树进行比较来测试原假设。然而，这种方法需要大量的计算工作（人和机器），并且结果取决于所做的进化假设。结果：我们提出了一个索引 I-cong，用于基于最大一致性子树（MAST）测试具有任意数量叶子的树之间的拓扑一致性。该指数简单明了、易于使用，不依赖于参数化进化事件的可能性，并提供相关的置信水平。
Motivation: Phylogenetic trees are omnipresent in evolutionary biology and the comparison of trees plays a central role there. Tree congruence statistics are based on the null hypothesis that two given trees are not more congruent (topologically similar) than expected by chance. Usually, one searches for the most parsimonious evolutionary scenario relating two trees and then one tests the null hypothesis by generating a high number of random trees and comparing these to the one between the observed trees. However, this approach requires a lot of computational work (human and machine) and the results depend on the evolutionary assumptions made.Results: We propose an index, I-cong, for testing the topological congruence between trees with any number of leaves, based on maximum agreement subtrees (MAST). This index is straightforward, simple to use, does not rely on parametrizing the likelihood of evolutionary events, and provides an associated confidence level.