UFBoot2: Improving the Ultrafast Bootstrap Approximation

Bouchenak-Khelladi, 2008, Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling, Mol Phylogenet Evol, 47, 488, 10.1016/j.ympev.2008.01.035

Chernomor, 2016, Terrace aware data structure for phylogenomic inference from supermatrices, Syst Biol, 65, 997, 10.1093/sysbio/syw037

Dell’Ampio, 2014, Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects, Mol Biol Evol, 31, 239, 10.1093/molbev/mst196

Efron, 1979, Bootstrap methods: another look at the jackknife, Ann Stat, 7, 1, 10.1214/aos/1176344552

Fabre, 2009, Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA, Mol Phylogenet Evol, 53, 808, 10.1016/j.ympev.2009.08.004

Felsenstein, 1981, Evolutionary trees from DNA sequences: a maximum likelihood approach, J Mol Evol, 17, 368, 10.1007/BF01734359

Felsenstein, 1985, Confidence limits on phylogenies : an approach using the bootstrap, Evolution (NY), 39, 783, 10.1111/j.1558-5646.1985.tb00420.x

Gadagkar, 2005, Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree, J Exp Zool B Mol Dev Evol, 304B, 64, 10.1002/jez.b.21026

Goldman, 1993, Statistical tests of models of DNA substitution, J Mol Evol, 36, 182, 10.1007/BF00166252

Guindon, 2010, New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol, 59, 307, 10.1093/sysbio/syq010

Hillis, 1993, An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis, Syst Biol, 42, 182, 10.1093/sysbio/42.2.182

Hinchliff, 2013, Using supermatrices for phylogenetic inquiry: an example using the sedges, Syst Biol, 62, 205, 10.1093/sysbio/sys088

Kishino, 1990, Maximum likelihood inference of protein phylogeny and the origin of chloroplasts, J Mol Evol, 31, 151, 10.1007/BF02109483

Minh, 2013, Ultrafast approximation for phylogenetic bootstrap, Mol Biol Evol, 30, 1188, 10.1093/molbev/mst024

Nguyen, 2015, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol Biol Evol, 32, 268, 10.1093/molbev/msu300

Nguyen, 2011, MISFITS: evaluating the goodness of fit between a phylogenetic model and an alignment, Mol Biol Evol, 28, 143, 10.1093/molbev/msq180

Nyakatura, 2012, Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates, BMC Biol, 10, 12., 10.1186/1741-7007-10-12

Pyron, 2011, The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees, Mol Phylogenet Evol, 58, 329, 10.1016/j.ympev.2010.11.006

Rambaut, 1997, Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, Bioinformatics, 13, 235, 10.1093/bioinformatics/13.3.235

Salichos, 2013, Inferring ancient divergences requires genes with strong phylogenetic signals, Nature, 497, 327, 10.1038/nature12130

Simmons, 2014, Divergent maximum-likelihood-branch-support values for polytomies, Mol Phylogenet Evol, 73, 87, 10.1016/j.ympev.2014.01.018

Springer, 2012, Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. Stanyon R, editor, PLoS One, 7, e49521., 10.1371/journal.pone.0049521

Stamatakis, 2006, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688, 10.1093/bioinformatics/btl446

Stamatakis, 2010, Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data, Bioinformatics, 26, i132, 10.1093/bioinformatics/btq205

Stamatakis, 2008, A rapid bootstrap algorithm for the RAxML web servers, Syst Biol, 57, 758, 10.1080/10635150802429642

Telford, 2015, Phylogenomic insights into animal evolution, Curr Biol, 25, R876, 10.1016/j.cub.2015.07.060

van der Linde, 2010, A supermatrix-based molecular phylogeny of the family Drosophilidae, Genet Res (Camb), 92, 25, 10.1017/S001667231000008X

Vinh, 2004, IQPNNI: moving fast through tree space and stopping in time, Mol Biol Evol, 21, 1565, 10.1093/molbev/msh176

Weiss, 2003, Testing substitution models within a phylogenetic tree, Mol Biol Evol, 20, 572, 10.1093/molbev/msg073

Whelan, 2006, PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees, Nucleic Acids Res, 34, D327, 10.1093/nar/gkj087

Whelan, 2010, The prevalence of multifurcations in tree-space and their implications for tree-search, Mol Biol Evol, 27, 2674, 10.1093/molbev/msq163