ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches
暂无分享,去创建一个
[1] David Posada,et al. SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees , 2015, bioRxiv.
[2] W. Maddison. Gene Trees in Species Trees , 1997 .
[3] Paramvir S. Dehal,et al. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.
[4] Noah A Rosenberg,et al. Gene tree discordance, phylogenetic inference and the multispecies coalescent. , 2009, Trends in ecology & evolution.
[5] D. Pearl,et al. Estimating species phylogenies using coalescence times among sequences. , 2009, Systematic biology.
[6] S. Edwards. IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? , 2009, Evolution; international journal of organic evolution.
[7] Elchanan Mossel,et al. Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci , 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[8] A. Rokas,et al. Contentious relationships in phylogenomic studies can be driven by a handful of genes , 2017, Nature Ecology &Evolution.
[9] M. Nei,et al. Relationships between gene trees and species trees. , 1988, Molecular biology and evolution.
[10] Tandy J. Warnow,et al. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes , 2015, Bioinform..
[11] Tandy Warnow,et al. Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting. , 2016, Systematic biology.
[12] Ziheng Yang,et al. INDELible: A Flexible Simulator of Biological Sequence Evolution , 2009, Molecular biology and evolution.
[13] A. Brachmann,et al. The effector candidate repertoire of the arbuscular mycorrhizal fungus Rhizophagus clarus , 2016, BMC Genomics.
[14] Tandy J. Warnow,et al. Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles , 2011, J. Comput. Biol..
[15] Tandy J. Warnow,et al. ASTRAL: genome-scale coalescent-based species tree estimation , 2014, Bioinform..
[16] Md. Shamsuzzoha Bayzid,et al. Statistical binning enables an accurate coalescent-based estimation of the avian tree , 2014, Science.
[17] D. Robinson,et al. Comparison of phylogenetic trees , 1981 .
[18] Raymond J. Moran,et al. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference , 2016, Genome biology and evolution.
[19] Pascal Frey,et al. Phylogenetic species recognition reveals host-specific lineages among poplar rust fungi. , 2013, Molecular phylogenetics and evolution.
[20] Md. Shamsuzzoha Bayzid,et al. Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses , 2014, PloS one.
[21] Tandy Warnow,et al. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer , 2015, bioRxiv.
[22] S. Tavaré. Some probabilistic and statistical problems in the analysis of DNA sequences , 1986 .
[23] Tandy Warnow,et al. On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods. , 2015, Systematic biology.
[24] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..
[25] Evgeny M. Zdobnov,et al. The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell , 2010, Bioinform..
[26] Liang Liu,et al. Estimating species trees from unrooted gene trees. , 2011, Systematic biology.
[27] Scott V Edwards,et al. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model , 2010, BMC Evolutionary Biology.
[28] Siavash Mirarab,et al. Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies , 2016, Molecular biology and evolution.
[29] Saravanaraj N. Ayyampalayam,et al. Phylotranscriptomic analysis of the origin and early diversification of land plants , 2014, Proceedings of the National Academy of Sciences.
[30] B. Faircloth,et al. Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods. , 2016, Systematic biology.
[31] 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.
[32] Gonzalo Giribet,et al. Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation , 2015, eLife.
[33] Siavash Mirarab,et al. Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction , 2016, BMC Genomics.
[34] John Gatesy,et al. The gene tree delusion. , 2016, Molecular phylogenetics and evolution.
[35] Md. Shamsuzzoha Bayzid,et al. Whole-genome analyses resolve early branches in the tree of life of modern birds , 2014, Science.
[36] Scott V Edwards,et al. Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. , 2016, Molecular phylogenetics and evolution.
[37] Laura Salter Kubatko,et al. Quartet Inference from SNP Data Under the Coalescent Model , 2014, Bioinform..
[38] Tandy Warnow,et al. ASTRID: Accurate Species TRees from Internode Distances , 2015, bioRxiv.
[39] Manuel Lafond,et al. On the Weighted Quartet Consensus problem , 2017, CPM.
[40] Edward L. Braun,et al. Error in Phylogenetic Estimation for Bushes in the Tree of Life , 2013 .
[41] Ziheng Yang,et al. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. , 2003, Genetics.
[42] first name surname. Upgrade compare article , 2012 .
[43] S. Carroll,et al. Genome-scale approaches to resolving incongruence in molecular phylogenies , 2003, Nature.
[44] A. Drummond,et al. Bayesian Inference of Species Trees from Multilocus Data , 2009, Molecular biology and evolution.
[45] John A Rhodes,et al. Determining species tree topologies from clade probabilities under the coalescent. , 2011, Journal of theoretical biology.
[46] John Gatesy,et al. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. , 2014, Molecular phylogenetics and evolution.