Computational approaches to species phylogeny inference and gene tree reconciliation.
Computational approaches to species phylogeny inference and gene tree reconciliation.
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DOI：
10.1016/j.tree.2013.09.004
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发表时间：
2013-12
影响因子：
16.8
通讯作者：
Nakhleh L
中科院分区：
文献类型：
--
作者：
Nakhleh L
基因树和物种遗传之间存在着错综复杂的关系，这是由于进化过程作用于物种遗传分支内和分支之间的基因。从分析的角度来看，基因树作为字符状态，推断准确的物种遗传，物种遗传作为一个背景，基因树的对比，阐明进化过程和参数。在1997年的一篇论文中，Maddison讨论了这种关系，回顾了基因树上三个主要进化过程留下的特征，并调查了利用这些特征来计算阐明这种关系的简约性和似然性标准。在这里，我们回顾了在这两个标准下开发计算方法进行分析所取得的进展，并调查剩余的挑战。
An intricate relationship exists between gene trees and species phylogenies, due to evolutionary processes that act on the genes within and across the branches of the species phylogeny. From an analytical perspective, gene trees serve as character states for inferring accurate species phylogenies, and species phylogenies serve as a backdrop against which gene trees are contrasted for elucidating evolutionary processes and parameters. In a 1997 paper, Maddison discussed this relationship, reviewed the signatures left by three major evolutionary processes on the gene trees, and surveyed parsimony and likelihood criteria for utilizing these signatures to computationally elucidate this relationship. Here, we review progress that has been made on developing computational methods for analyses under these two criteria, and survey remaining challenges.
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影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
影响因子：
10.7
作者：
Cohen, Ofir;Gophna, Uri;Pupko, Tal
通讯作者：
Pupko, Tal
基因树进化的最大似然模型和算法，并具有重复和损失。
影响因子：
3
作者：
Górecki P;Burleigh GJ;Eulenstein O
通讯作者：
Eulenstein O
影响因子：
6.5
作者：
Chung, Yujin;Ane, Cecile
通讯作者：
Ane, Cecile
影响因子：
1.1
作者：
Bordewich, Magnus;Semple, Charles
通讯作者：
Semple, Charles