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IQ-TREE Version 2.1.2: Tutorials and Manual Phylogenomic Software by Maximum Likelihood

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IQ-TREE version 2.1.2: Tutorials and Manual Phylogenomic software by maximum likelihood http://www.iqtree.org Bui Quang Minh, Rob Lanfear, Jana Trifinopoulos, Dominik Schrempf, Heiko A. Schmidt March 15, 2021 2 Preface Contents 1 Introduction 9 1.1 Why IQ-TREE? .............................. 9 1.2 Key features ................................. 10 1.3 Free web server ............................... 10 1.4 User support ................................ 11 1.5 Documentation ............................... 11 1.6 How to cite IQ-TREE? ........................... 12 1.7 Development team ............................. 13 1.8 Credits and acknowledgements ....................... 14 2 Getting started 15 2.1 IQ-TREE web server ............................ 15 2.2 Installation ................................. 15 2.2.1 Packages and bundles ....................... 15 2.2.2 Manual download .......................... 16 2.3 For Windows users ............................. 16 2.4 For Mac OS X users ............................ 16 2.5 Minimal command-line examples ..................... 17 2.6 Where to go from here? .......................... 20 3 Web server tutorial 21 3.1 Tree Inference ................................ 21 3.2 Model Selection ............................... 23 3.3 Analysis Results .............................. 23 4 Beginner’s tutorial 27 4.1 Input data .................................. 27 4.2 First running example ........................... 28 4.3 Choosing the right substitution model .................. 30 4.4 Using codon models ............................ 32 3 4 CONTENTS 4.5 Binary, morphological and SNP data ................... 33 4.6 Assessing branch supports with ultrafast bootstrap approximation ... 34 4.7 Reducing impact of severe model violations with UFBoot ........ 35 4.8 Assessing branch supports with standard nonparametric bootstrap ... 35 4.9 Assessing branch supports with single branch tests ........... 35 4.10 Utilizing multi-core CPUs ......................... 37 4.11 Where to go from here? .......................... 38 5 Advanced tutorial 39 5.1 Partitioned analysis for multi-gene alignments .............. 39 5.2 Partitioned analysis with mixed data ................... 41 5.3 Choosing the right partitioning scheme .................. 42 5.4 Ultrafast bootstrapping with partition model ............... 43 5.5 Constrained tree search .......................... 43 5.6 Tree topology tests ............................. 45 5.7 Testing constrained tree .......................... 46 5.8 Consensus construction and bootstrap value assignment ......... 48 5.9 User-defined substitution models ..................... 49 5.10 Inferring site-specific rates ......................... 50 5.11 Where to go from here? .......................... 52 6 Assessing phylogenetic assumptions 53 6.1 Tests of symmetry ............................. 53 6.2 Likelihood mapping ............................. 55 7 Concordance Factor 59 7.1 Inferring species tree ............................ 60 7.2 Inferring gene/locus trees ......................... 60 7.3 Gene concordance factor (gCF) ...................... 61 7.4 Site concordance factor (sCF) ....................... 61 7.5 Putting it all together ........................... 62 8 Phylogenetic Dating 63 8.1 Inferring time tree with tip dates ..................... 64 8.2 Calibrating tree using ancestral dates ................... 66 8.3 Dating an existing tree ........................... 67 8.4 Obtaining confidence intervals ....................... 67 8.5 Excluding outlier taxa/nodes ....................... 67 8.6 Full list of LSD2 options .......................... 68 9 Rooting phylogenetic trees 75 CONTENTS 5 9.1 Inferring unrooted tree with outgroup ................... 75 9.2 Inferring rooted trees without outgroup .................. 77 9.3 Testing root positions ........................... 80 10 Command reference 83 10.1 General options ............................... 83 10.1.1 Example usages: .......................... 85 10.2 Checkpointing to resume stopped run ................... 85 10.3 Likelihood mapping analysis ........................ 86 10.3.1 Example usages: .......................... 87 10.4 Automatic model selection ......................... 89 10.4.1 Example usages: .......................... 92 10.5 Specifying substitution models ....................... 93 10.5.1 Example usages: .......................... 94 10.6 Rate heterogeneity ............................. 94 10.7 Partition model options .......................... 95 10.8 Site-specific frequency model options ................... 96 10.9 Tree search parameters ........................... 96 10.9.1 Example usages: .......................... 98 10.10Ultrafast bootstrap parameters ...................... 98 10.10.1 Example usages: .......................... 99 10.11Nonparametric bootstrap .......................... 99 10.12Single branch tests ............................. 99 10.12.1 Example usages: .......................... 100 10.13Ancestral sequence reconstruction ..................... 100 10.13.1 Example usages: .......................... 100 10.14Tree topology tests ............................. 101 10.14.1 Example usages: .......................... 102 10.15Constructing consensus tree ........................ 102 10.16Computing Robinson-Foulds distance ................... 103 10.16.1 Example usages: .......................... 103 10.17Generating random trees .......................... 104 10.17.1 Example usages: .......................... 104 10.18Miscellaneous options ............................ 104 10.18.1 Example usages: .......................... 105 11 Substitution models 109 11.1 DNA models ................................ 109 11.1.1 Base substitution rates ....................... 109 11.1.2 Base frequencies .......................... 111 11.1.3 Lie Markov models ......................... 111 6 CONTENTS 11.2 Protein models ............................... 113 11.2.1 Amino-acid exchange rate matrices ................ 113 11.2.2 Protein mixture models ...................... 114 11.2.3 User-defined empirical protein models .............. 115 11.2.4 Amino-acid frequencies ....................... 116 11.3 Codon models ................................ 116 11.3.1 Codon substitution rates ...................... 117 11.3.2 Codon frequencies ......................... 118 11.4 Binary and morphological models ..................... 119 11.5 Ascertainment bias correction ....................... 119 11.6 Rate heterogeneity across sites ....................... 120 12 Complex models 121 12.1 Partition models .............................. 121 12.1.1 Partition file format ........................ 122 12.1.2 Partitioned analysis ........................ 124 12.2 Mixture models ............................... 124 12.2.1 What is the difference between partition and mixture models? . 124 12.2.2 Defining mixture models ...................... 124 12.2.3 Profile mixture models ....................... 125 12.2.4 NEXUS model file ......................... 126 12.3 Site-specific frequency models ....................... 127 12.3.1 Example usages ........................... 128 12.4 Heterotachy models ............................. 129 12.4.1 Quick usages ............................ 129 13 Polymorphism-aware models 131 13.1 Counts files ................................. 132 13.1.1 Conversion scripts ......................... 132 13.2 First running example ........................... 133 13.3 Substitution models ............................ 133 13.4 Virtual population size ........................... 134 13.5 Level of polymorphism ........................... 134 13.6 Sampling method .............................. 135 13.7 State frequency type ............................ 135 13.8 Rate heterogeneity ............................. 136 13.9 Bootstrap branch support ......................... 136 13.10Interpretation of branch lengths ...................... 136 14 Compilation guide 139 14.1 General requirements ............................ 139 CONTENTS 7 14.2 Downloading source code .......................... 140 14.3 Compiling under Linux ........................... 140 14.4 Compiling under Mac OS X ........................ 141 14.5 Compiling under Windows ......................... 142 14.6 Compiling 32-bit version .......................... 143 14.7 Compiling MPI version ........................... 144 14.8 Compiling Xeon Phi Knights Landing version .............. 145 14.9 About precompiled binaries ........................ 145 14.10Setup an Xcode project in MacOS ..................... 146 14.11This will generate a a subfolder build-xcode/iqtree.xcodeproj, which you can open in Xcode now. .................... 147 15 Frequently asked questions 149 15.1 How do I get help? ............................. 149 15.2 How do I report bug? ............................ 149 15.3 How do I interpret ultrafast bootstrap (UFBoot) support values? ... 150 15.4 How does IQ-TREE treat gap/missing/ambiguous characters? ..... 150 15.5 Can I mix DNA and protein data in a partitioned analysis? ...... 151 15.6 What is the interpretation of branch lengths when mixing codon and DNA data? ................................. 152 15.7 What is the purpose of composition test? ................. 152 15.8 What is the good number of CPU cores to use? ............. 153 15.9 How do I save time for standard bootstrap? ............... 154 15.10Why does IQ-TREE complain about the use of +ASC model? ..... 155 15.11How does IQ-TREE treat identical sequences? .............. 156 15.12What are the
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