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layout: userdoc title: | IQ-TREE version 2.1.2: Tutorials and Manual Phylogenomic software by maximum likelihood
subtitle: "http://www.iqtree.org"
author: |
Bui Quang Minh, Rob Lanfear,
Jana Trifinopoulos, Dominik Schrempf, Heiko A. Schmidt
date: March 15, 2021 keywords: [phylogenomic inference, maximum likelihood] toc: true papersize: A4 documentclass: book margin-left: 1in margin-right: 1.2in fontsize: 12pt linkcolor: blue urlcolor: blue toccolor: black institute: Australian National University, https://www.anu.edu.au include-before: | Preface
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Copyright (c) 2010-2016 IQ-TREE development team.
- First example
- Model selection
- New model selection
- Codon models
- Binary, Morphological, SNPs
- Ultrafast bootstrap
- Nonparametric bootstrap
- Single branch tests
- Partitioned analysis
- Partitioning with mixed data
- Partition scheme selection
- Bootstrapping partition model
- Utilizing multi-core CPUs
- Tree topology tests
- User-defined models
- Consensus construction and bootstrap value assignment
- Computing Robinson-Foulds distance
- Generating random trees
- DNA models
- Protein models
- Codon models
- Binary, morphological models
- Ascertainment bias correction
- Rate heterogeneity
- Counts files
- First running example
- Substitution models
- Virtual population size
- Sampling method
- Bootstrap branch support
- Interpretation of branch lengths