IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Chor, 2005, Maximum likelihood of evolutionary trees is hard, Lect Notes Comput Sci., 3500, 296, 10.1007/11415770_23

Farris, 1970, Methods for computing Wagner trees, Syst Zool., 19, 83, 10.2307/2412028

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

Felsenstein, 2004, Inferring phylogenies

Fitch, 1971, Toward defining course of evolution—minimum change for a specific tree topology, Syst Zool., 20, 406, 10.2307/2412116

Flouri, 2014, The phylogenetic likelihood library, Syst Biol.

Gascuel, 1997, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Mol Biol Evol., 14, 685, 10.1093/oxfordjournals.molbev.a025808

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

Guindon, 2003, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst Biol., 52, 696, 10.1080/10635150390235520

Helaers, 2010, MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics, BMC Bioinformatics, 11, 379, 10.1186/1471-2105-11-379

Hordijk, 2005, Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood, Bioinformatics, 21, 4338, 10.1093/bioinformatics/bti713

Lanave, 1984, A new method for calculating evolutionary substitution rates, J Mol Evol., 20, 86, 10.1007/BF02101990

Lewis, 1998, A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data, Mol Biol Evol., 15, 277, 10.1093/oxfordjournals.molbev.a025924

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

Minh, 2005, pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies, Bioinformatics, 21, 3794, 10.1093/bioinformatics/bti594

Money, 2012, Characterizing the phylogenetic tree-search problem, Syst Biol., 61, 228, 10.1093/sysbio/syr097

Morrison, 2007, Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences, Syst Biol., 56, 988, 10.1080/10635150701779808

Rechenberg, 1973, Evolutionsstrategie—optimierung technischer systeme nach prinzipien der biologischen evolution

Salter, 2001, Stochastic search strategy for estimation of maximum likelihood phylogenetic trees, Syst Biol., 50, 7, 10.1080/106351501750107413

Sanderson, 1994, TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life, Am J Bot., 81, 183

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

Swofford, 2003, PAUP*. Phylogenetic analysis using parsimony (* and other methods)

Swofford, 1990, Phylogeny reconstruction, Molecular systematics, 411

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

Vos, 2003, Accelerated likelihood surface exploration: the likelihood ratchet, Syst Biol., 52, 368, 10.1080/10635150390196993

Whelan, 2001, A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach, Mol Biol Evol., 18, 691, 10.1093/oxfordjournals.molbev.a003851

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

Yang, 1994, Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods, J Mol Evol., 39, 306, 10.1007/BF00160154

Yang, 2000, Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A, J Mol Evol., 51, 423, 10.1007/s002390010105

Zwickl DJ Genetic algorithm approaches for the phylogenetic analysis of large biological sequence data sets under the maximum likelihood criterion 2006 [Ph.D. dissertation]. Austin (TX): The University of Texas at Austin