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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 examples that combine IQ-TREE with other software. sections_new_page: True sections:
- name: Phylogenetic placement url: phylogenetic-placement
- name: Perform a Goldman-Cox test url: goldman-cox-test
- name: Estimating gene, site, and quartet concordance vectors url: concordance-vector
This is a collection of detailed examples analyses that combine IQ-TREE with other bits of code and/or software (hence 'recipes'). They are an attempt to go a bit beyond the usual user docs for software, getting closer to end-to-end analyses. 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, and describe in as much detail as possible (with references and example data if you can) what it is you would like.
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
- 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