L.U.St: a tool for approximated maximum likelihood supertree reconstruction
暂无分享,去创建一个
Mark D. Wilkinson | Christopher J. Creevey | Davide Pisani | Wasiu A. Akanni | M. Wilkinson | C. Creevey | D. Pisani
[1] B. Baum. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees , 1992 .
[2] Hidetoshi Shimodaira,et al. Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference , 1999, Molecular Biology and Evolution.
[3] Masatoshi Nei,et al. Reanalysis of Murphy et al.’s Data Gives Various Mammalian Phylogenies and Suggests Overcredibility of Bayesian Trees , 2003, Journal of Molecular Evolution.
[4] Masami Hasegawa,et al. CONSEL: for assessing the confidence of phylogenetic tree selection , 2001, Bioinform..
[5] James O. McInerney,et al. Clann: investigating phylogenetic information through supertree analyses , 2005, Bioinform..
[6] Thérèse A. Holton,et al. Deep Genomic-Scale Analyses of the Metazoa Reject Coelomata: Evidence from Single- and Multigene Families Analyzed Under a Supertree and Supermatrix Paradigm , 2010, Genome biology and evolution.
[7] François-Joseph Lapointe,et al. Matrix representations with parsimony or with distances: two sides of the same coin? , 2003, Systematic biology.
[8] M. Ragan. Phylogenetic inference based on matrix representation of trees. , 1992, Molecular phylogenetics and evolution.
[9] H. Philippe,et al. Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study. , 2013, Systematic biology.
[10] Mike A. Steel,et al. Computing the Distribution of a Tree Metric , 2009, IEEE ACM Trans. Comput. Biol. Bioinform..
[11] Charles Semple,et al. A supertree method for rooted trees , 2000, Discret. Appl. Math..
[12] Frédéric Delsuc,et al. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. , 2013, Molecular biology and evolution.
[13] T Martin Embley,et al. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods , 2009, Philosophical Transactions of the Royal Society B: Biological Sciences.
[14] D. Robinson,et al. Comparison of phylogenetic trees , 1981 .
[15] M. Gouy,et al. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. , 2002, Genome research.
[16] Mark Wilkinson,et al. Majority-rule supertrees. , 2007, Systematic biology.
[17] A. D. Gordon. Consensus supertrees: The synthesis of rooted trees containing overlapping sets of labeled leaves , 1986 .
[18] M. Hasegawa,et al. Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data. , 2000, Gene.
[19] Jason E Stajich,et al. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis , 2006, BMC Evolutionary Biology.
[20] Alfred V. Aho,et al. Inferring a Tree from Lowest Common Ancestors with an Application to the Optimization of Relational Expressions , 1981, SIAM J. Comput..
[21] Andy Purvis,et al. A Modification to Baum and Ragan's Method for Combining Phylogenetic Trees , 1995 .
[22] O. Bininda-Emonds. Phylogenetic Supertrees: Combining Information To Reveal The Tree Of Life , 2004 .
[23] Sen Song,et al. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model , 2012, Proceedings of the National Academy of Sciences.
[24] François-Joseph Lapointe,et al. Properties of supertree methods in the consensus setting. , 2007, Systematic biology.
[25] Mike Steel,et al. Maximum likelihood supertrees. , 2007, Systematic biology.
[26] Hidetoshi Shimodaira. An approximately unbiased test of phylogenetic tree selection. , 2002, Systematic biology.
[27] R. Ward,et al. Mitochondrial genes and mammalian phylogenies: increasing the reliability of branch length estimation. , 2000, Molecular biology and evolution.
[28] Andrea L. Cirranello,et al. The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals , 2013, Science.
[29] Davide Pisani,et al. Supertrees disentangle the chimerical origin of eukaryotic genomes. , 2007, Molecular biology and evolution.
[30] H. Kishino,et al. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea , 1989, Journal of Molecular Evolution.
[31] M. Springer,et al. A Critique of Matrix Representation with Parsimony Supertrees , 2004 .
[32] J. McInerney,et al. Heterogeneous Models Place the Root of the Placental Mammal Phylogeny , 2013, Molecular biology and evolution.
[33] Nicholas G. Crawford,et al. LSU Digital Commons LSU Digital Commons Ultraconserved elements are novel phylogenomic markers that Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with resolve placental mammal phylogeny when combined with species-tree analysis species-tr , 2022 .
[34] G. Edgecombe,et al. A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata , 2011, Proceedings of the Royal Society B: Biological Sciences.
[35] T. J. Robinson,et al. Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification , 2011, Science.
[36] Simon A. A. Travers,et al. Does a tree–like phylogeny only exist at the tips in the prokaryotes? , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[37] James O. McInerney,et al. Some Desiderata for Liberal Supertrees , 2004 .