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Developer Guide
minh edited this page Dec 1, 2015
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This developers' guide gives an overview of IQ-TREE code.
To achieve both high performance and flexibility, IQ-TREE software has been entirely written in object oriented C++. Thus, it faciliates extending with new sequence data types or new models. IQ-TREE code consists of C++ classes, most of which inherits from three basal classes: Alignment, ModelSubst and PhyloTree to handle sequence alignment, model of substitution and phylogenetic tree, respectively.
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