New Methods to Calculate Concordance Factors for Phylogenomic Datasets
New Methods to Calculate Concordance Factors for Phylogenomic Datasets
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DOI：
10.1093/molbev/msaa106
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发表时间：
2020-09-01
影响因子：
10.7
通讯作者：
Lanfear, Robert
中科院分区：
文献类型：
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作者：
Bui Quang Minh;Hahn, Matthew W.;Lanfear, Robert
我们实施了两种量化系统发育数据集中谱系一致性的方法：基因一致性因子（gCF）和新位点一致性因子（sCF）。对于参考树的每个分支，gCF 被定义为包含该分支的“决定性”基因树的百分比。这种测量方法已经被广泛使用，但在这里我们引入了一个包，可以在考虑基因树之间可变分类单元覆盖的同时进行计算。 sCF 是一种新的衡量标准，定义为参考树中支持分支的决定性位点的百分比。 gCF 和 sCF 通过提供基因座和位点之间潜在分歧的完整描述来补充系统发育学中分支支持的经典测量。 IQ-TREE 软件包中免费提供易于使用的实现和教程（http://www.iqtree.org/doc/Concordance-Factor，上次访问时间为 2020 年 5 月 13 日）。
We implement two measures for quantifying genealogical concordance in phylogenomic data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of "decisive" gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org/doc/Concordance-Factor, last accessed May 13, 2020).