Practical Aspects of Phylogenetic Network Analysis Using PhyloNet
暂无分享,去创建一个
Xinhao Liu | Zhi Yan | Zhen Cao | Luay Nakhleh | Huw A. Ogilvie | L. Nakhleh | H. Ogilvie | Zhi Yan | Zhen Cao | Xinhao Liu | Luay K. Nakhleh
[1] Luay Nakhleh,et al. Supplementary Information : Co-estimating Reticulate Phylogenies and Gene Trees from Multi-locus Sequence Data , 2017 .
[2] Michael DeGiorgio,et al. Robustness to divergence time underestimation when inferring species trees from estimated gene trees. , 2014, Systematic biology.
[3] L. Nakhleh. Evolutionary Phylogenetic Networks: Models and Issues , 2010 .
[4] W. Maddison,et al. Inferring phylogeny despite incomplete lineage sorting. , 2006, Systematic biology.
[5] Vincent Moulton,et al. Inferring polyploid phylogenies from multiply-labeled gene trees , 2009, BMC Evolutionary Biology.
[6] Jiafan Zhu,et al. Inference of species phylogenies from bi-allelic markers using pseudo-likelihood , 2018, bioRxiv.
[7] Gabriel Cardona,et al. Comparison of Galled Trees , 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[8] Katharina T. Huber,et al. Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[9] A. von Haeseler,et al. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.
[10] Bengt Oxelman,et al. Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. , 2012, Systematic biology.
[11] Richard R. Hudson,et al. Generating samples under a Wright-Fisher neutral model of genetic variation , 2002, Bioinform..
[12] Gabriel Cardona,et al. On Nakhleh's Metric for Reduced Phylogenetic Networks , 2009, TCBB.
[13] J. Degnan,et al. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. , 2016, Systematic biology.
[14] Luay Nakhleh,et al. Inferring Phylogenetic Networks Using PhyloNet , 2017, bioRxiv.
[15] J. Felsenstein,et al. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. , 1994, Molecular biology and evolution.
[16] Luay Nakhleh,et al. Species Tree Inference by Minimizing Deep Coalescences , 2009, PLoS Comput. Biol..
[17] J. Mallet. Hybridization as an invasion of the genome. , 2005, Trends in ecology & evolution.
[18] Gabriel Cardona,et al. Two Results on Distances for Phylogenetic Networks , 2010, IWPACBB.
[19] Juan Wang,et al. A review of metrics measuring dissimilarity for rooted phylogenetic networks , 2019, Briefings Bioinform..
[20] Luay Nakhleh,et al. Empirical Performance of Tree-based Inference of Phylogenetic Networks , 2019, bioRxiv.
[21] Matthew W. Hahn,et al. Gene-tree reconciliation with MUL-trees to resolve polyploidy events , 2016, bioRxiv.
[22] Christoph Oberprieler,et al. A permutation approach for inferring species networks from gene trees in polyploid complexes by minimising deep coalescences , 2017 .
[23] Yun Yu,et al. Bayesian inference of phylogenetic networks from bi-allelic genetic markers , 2017, bioRxiv.
[24] Joseph K. Pickrell,et al. Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data , 2012, PLoS genetics.
[25] Claudia R. Solís-Lemus,et al. Inconsistency of Species Tree Methods under Gene Flow. , 2016, Systematic biology.
[26] Céline Scornavacca,et al. Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable , 2015, PLoS Comput. Biol..
[27] W. Maddison. Gene Trees in Species Trees , 1997 .
[28] Luay Nakhleh,et al. Co-estimating Reticulate Phylogenies and Gene Trees from Multi-locus Sequence Data , 2017, bioRxiv.
[29] Gabriel Cardona,et al. The Comparison of Tree-Sibling Time Consistent Phylogenetic Networks Is Graph Isomorphism-Complete , 2014, TheScientificWorldJournal.
[30] Yun Yu,et al. Fast algorithms and heuristics for phylogenomics under ILS and hybridization , 2013, BMC Bioinformatics.
[31] J. McInerney,et al. The public goods hypothesis for the evolution of life on Earth , 2011, Biology Direct.
[32] L. Nakhleh,et al. A Metric on the Space of Reduced Phylogenetic Networks , 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[33] Xinhao Liu,et al. A divide-and-conquer method for scalable phylogenetic network inference from multilocus data , 2019, bioRxiv.
[34] Katharina T. Huber,et al. Folding and unfolding phylogenetic trees and networks , 2015, Journal of mathematical biology.
[35] P. Smouse,et al. genalex 6: genetic analysis in Excel. Population genetic software for teaching and research , 2006 .
[36] Huw A. Ogilvie,et al. Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization , 2018, Bioinformatics and Phylogenetics.
[37] Chao Zhang,et al. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees , 2018, BMC Bioinformatics.
[38] Yun Yu,et al. In the light of deep coalescence: revisiting trees within networks , 2016, BMC Bioinformatics.
[39] Luay Nakhleh,et al. The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection , 2012, PLoS genetics.
[40] L. Nakhleh,et al. Integrated likelihood for phylogenomics under a no-common-mechanism model , 2018, BMC Genomics.
[41] Luay Nakhleh,et al. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships , 2008, BMC Bioinformatics.
[42] P. Donnelly,et al. Inference of population structure using multilocus genotype data. , 2000, Genetics.
[43] Noah A. Rosenberg,et al. Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences , 2011, J. Comput. Biol..
[44] Yun Yu,et al. A maximum pseudo-likelihood approach for phylogenetic networks , 2015, BMC Genomics.
[45] Huw A. Ogilvie,et al. Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods , 2015, Systematic biology.
[46] Bin Ma,et al. From Gene Trees to Species Trees , 2000, SIAM J. Comput..
[47] Joseph K. Pickrell,et al. Toward a new history and geography of human genes informed by ancient DNA. , 2014, Trends in genetics : TIG.
[48] M. Stephens,et al. Inference of population structure using multilocus genotype data: dominant markers and null alleles , 2007, Molecular ecology notes.
[49] Noah A Rosenberg,et al. Gene tree discordance, phylogenetic inference and the multispecies coalescent. , 2009, Trends in ecology & evolution.
[50] Kevin J. Liu,et al. Maximum likelihood inference of reticulate evolutionary histories , 2014, Proceedings of the National Academy of Sciences.
[51] Alberto Policriti,et al. GAM-NGS: genomic assemblies merger for next generation sequencing , 2013, BMC Bioinformatics.
[52] Nava Levit-Binnun,et al. A quantitative physical model of the TMS-induced discharge artifacts in EEG , 2018, PLoS Comput. Biol..
[53] Luay Nakhleh,et al. Parsimonious inference of hybridization in the presence of incomplete lineage sorting. , 2013, Systematic biology.
[54] Bengt Oxelman,et al. Phylogenetics of Allopolyploids , 2017 .