Multiple consensus trees: a method to separate divergent genes.
Multiple consensus trees: a method to separate divergent genes.
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DOI：
10.1186/1471-2105-14-46
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发表时间：
2013-02-09
影响因子：
3
通讯作者：
Guénoche A
中科院分区：
文献类型：
--
作者：
Guénoche A
人们普遍承认，物种树不能从单个基因的遗传序列中推断出来，因为不同基因的进化以及基因树的拓扑结构可能会有很大的不同。基因树可以不同，例如，因为水平转移事件或因为它们中的一些对应于旁系同源而不是直系同源序列。为了重建物种树，已经提出了各种方法来解决基因树的调和问题。当所有树中的类群相同时，问题可以被描述为共识树问题。在本文中，我们定义了一个新的方法来决定是否唯一的共识树或多个共识树可以最好地代表一组给定的系统发育树。如果给定的树都是全等的，它们应该兼容成一个单一的共识树。否则，可以识别对应于不同遗传模式的几个共有树。我们介绍了一种方法优化广义得分，在一组树的分区，以决定是否给定的基因树是同质的或不。该方法已被验证与模拟数据（随机树组织在三个拓扑群）以及与真实的数据（引导树，同质树集，和一组非同质基因树的30 E.大肠杆菌菌株;值得注意的是，后者的一些基因经历了水平基因转移）。研究界可免费获得用C编写的计算机程序MCT -多重共识树（可从http：//bioinformatics.lif.univ-mrs.fr/consensus/index.html下载）。它以标准的Newick格式处理树，建立三个层次对应于树之间的RF和QS相似性和贪婪上升算法。计算所有树分区的广义得分值。
It is generally admitted that the species tree cannot be inferred from the genetic sequences of a single gene because the evolution of different genes, and thus the gene tree topologies, may vary substantially. Gene trees can differ, for example, because of horizontal transfer events or because some of them correspond to paralogous instead of orthologous sequences. A variety of methods has been proposed to tackle the problem of the reconciliation of gene trees in order to reconstruct a species tree. When the taxa in all the trees are identical, the problem can be stated as a consensus tree problem. In this paper we define a new method for deciding whether a unique consensus tree or multiple consensus trees can best represent a set of given phylogenetic trees. If the given trees are all congruent, they should be compatible into a single consensus tree. Otherwise, several consensus trees corresponding to divergent genetic patterns can be identified. We introduce a method optimizing the generalized score, over a set of tree partitions in order to decide whether the given set of gene trees is homogeneous or not. The proposed method has been validated with simulated data (random trees organized in three topological groups) as well as with real data (bootstrap trees, homogeneous set of trees, and a set of non homogeneous gene trees of 30 E. Coli strains; it is worth noting that some of the latter genes underwent horizontal gene transfers). A computer program, MCT - Multiple Consensus Trees, written in C was made freely available for the research community (it can be downloaded from http://bioinformatics.lif.univ-mrs.fr/consensus/index.html). It handles trees in a standard Newick format, builds three hierarchies corresponding to RF and QS similarities between trees and the greedy ascending algorithm. The generalized score values of all tree partitions are computed.
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影响因子：
3
作者：
Koperwas J;Walczak K
通讯作者：
Walczak K
DOI：
10.2307/2413326
发表时间：
1985-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
ESTABROOK, GF;MCMORRIS, FR;MEACHAM, CA
通讯作者：
MEACHAM, CA
影响因子：
10.7
作者：
de Vienne, Damien M.;Ollier, Sebastien;Aguileta, Gabriela
通讯作者：
Aguileta, Gabriela
影响因子：
6.5
作者：
Bonnard, Cecile;Berry, Vincent;Lartillot, Nicolas
通讯作者：
Lartillot, Nicolas
影响因子：
2
作者：
Darlu, Pierre;Guenoche, Alain
通讯作者：
Guenoche, Alain