# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz The number and diversity of tree comparison methods and software have substantially increased in the last few years. The tree comparison methods variously use tree bipartitions , such as partition, or symmetric difference metrics (11) and split distance (12); distance between nodes such as the path length metrics (13), nodal distance (12, 14) and nodal distance for rooted trees (15); comparison of evolutionary units such as triplets and quartets (16); subtransfer operations such as subtree transfer distance (17), nearest-neighbor interchanging (18), Subtree Prune and Regraft (SPR) using a rooted reference tree (19), SPR for unrooted trees (20) and Tree Bisection and Reconnection (TBR) (17); (dis)agreement methods such as agreement subtrees (21), disagree (12), corresponding mapping (22) and congruence index (23); tree reconciliation (24); and topological and branch lengths methods such as K-tree score (25). Several algorithms have been proposed to analyze with multi-family trees. For example,the FMTS algorithm systematically prunes each gene copy from a multi-family tree to obtain all possible single-gene trees (12) and an algorithm implemented in TreeKO prunes nodes from the input rooted trees in which duplication and speciation events are labeled (26).However, to the best of our knowledge, none of the available metrics for tree comparison takes into account the robustness of the branches, a feature that appears important to minimize the impact of artefacts (unreliable parts of a tree) on the outcome of comparative tree analysis. Here, we present the Boot-Split Distance (BSD) method that calculates distances between phylogenetic trees with weighting based on bootstrap values. This method is implemented in the program TOPD/FMTS (12). In our recent research, we used the BSD method combined with classical multidimensional scaling (CMDS) analysis to explore the main trends in the phylogenetic FOL and to explore the “Tree of Life” (TOL) concept in light of comparative genomics (5, 27). 在过去几年中，比较系统发育树的方法和软件的数量和类型大幅增加。树的比较方法不同地使用树的二分法，如分割、对称差分度量（ 11 ）和分裂距离（ 12 ）；节点之间的距离，如路径长度度量（ 13 ）、节点距离（ 12 、 14 ）和定根树节点距离（ 15 ）；进化单位的比较，如三元组和四元组（ 16 ）；亚树交换距离（ 17 ）、最近邻交换（ 18 ）、使用有根参考树（ 19 ）的亚树修剪和重新生成（ SPR ）、无根树的亚树修剪和重新生成（ 20 ）和发育树切分和重新连接（ TBR ）（ 17 ）等操作；（ dis ）一致方法，如一致亚树（ 21 ）、不一致法（ 12 ）、对应映射（ 22 ）和一致指数（ 23 ）；树协调（ 24 ）；拓扑和分支长度方法，如 k- 树评分（ 25 ）。几种多族树分析的算法被提出，例如， FMTS 算法系统地从多族树中剪除每个基因拷贝，以获得所有可能的单基因树（ 12 ）， TreeKO 中实现的算法从输入的有根树中修剪节点，对基因重复和物种形成事件进行标记（ 26 ）。然而，据我们所知，所有可用的树比较指标都没有考虑到分支的稳健性，这一特性对于最小化人为误差（树的不可靠部分）对比较树分析结果的影响似乎很重要。在此，我们提出了基于自举检验值加权的系统树间距离计算方法。该方法集成在 TOPD/FMTS （ 12 ）程序中。在我们最近的研究中，我们使用 BSD 方法结合经典多维尺度分析（ CMDS ）来探索系统发育的主要趋势，并根据比较基因组学（ 5 ， 27 ）来探索“生命树”（ TOL ）概念。 Pere Puigbò, Wolf Y I , Koonin E V . Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life . Methods in Molecular Biology.
标签: 比较树
