Reconstructing evolutionary graphs: 3D parsimony
Reconstructing evolutionary graphs: 3D parsimony
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DOI：
10.1093/molbev/msn117
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发表时间：
2008-08-01
影响因子：
10.7
通讯作者：
Lake, James A.
中科院分区：
文献类型：
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作者：
Lake, James A.
越来越多的人认识到共生通过基因组融合极大地改变了进化，这就需要能够可靠地检测和重建融合的算法。在这里，我们推广了bootstrappers gambit算法（一种四重奏方法），以便允许它在单个数学模型下分析分叉和融合，从而检测过去的基因组分支和内共生。这种新的方法，三维简约，可以应用于对齐序列，如基因，indel，或其他基因组存在/缺失序列。它还为每个可能的图提供支持的统计度量。将该方法应用于生命环，证明了它的有效性。
The increasing recognition that symbioses have greatly altered evolution through genome fusions is creating a need for algorithms that can reliably detect and reconstruct fusions. Here, we generalize the bootstrappers gambit algorithm (a quartet method) in order to permit it to analyze both bifurcations and fusions under a single mathematical model, and thereby detect past genomic branchings and endosymbioses. This new method, 3-dimensional parsimony, can be applied to aligned sequences, such as gene, indel, or other genomic presence/absence sequences. It also provides a statistical measure of support for each possible graph. The usefulness of this method is demonstrated by applying it to the ring of life.