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Minh Bui edited this page Jun 25, 2024
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layout: userdoc title: "Recipes (How-To)" author: AUTHOR date: DATE docid: 9.5 icon: question-circle doctype: manual tags:
- manual description: Collection of one-off examples of analyses in IQ-TREE. sections_new_page: True sections:
- name: Phylogenetic placement url: phylogenetic-placement
- name: Perform a Goldman-Cox test url: goldman-cox-test
This is a collection of one-off examples of analyses in IQ-TREE.
One might call them "infrequently asked questions". The idea is a searchable and reproducible database of analyses to help the community do what they need to with IQ-TREE.
If you'd like to request a recipe, please head over to the issues page and use the 'recipe wanted' label.
Copyright (c) 2010-2022 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
- Estimating amino acid substitution models
- DNA models
- Protein models
- 3Di and TEA 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