Linux command
iqtree 命令
文本
复制后可按需替换文件名、目录或参数。
常用示例
Run phylogenetic analysis
iqtree -s [alignment.fasta]
Specify model
iqtree -s [alignment.fasta] -m [GTR+G]
Automatic model selection
iqtree -s [alignment.fasta] -m MFP
Standard bootstrap analysis
iqtree -s [alignment.fasta] -b [1000]
Ultra-fast bootstrap
iqtree -s [alignment.fasta] -B [1000]
Use multiple threads
iqtree -s [alignment.fasta] -T [4]
说明
IQ-TREE is a phylogenetic analysis tool for maximum likelihood tree inference. It supports various substitution models, model selection, and multiple bootstrap methods. IQ-TREE is known for its speed and accuracy, implementing efficient algorithms for large-scale phylogenetic analysis. It handles DNA, protein, codon, and morphological data.
参数
- -s _file_
- Input alignment file.
- -m _model_
- Substitution model (or MFP for selection).
- -b _n_
- Standard bootstrap replicates.
- -B, --ufboot _n_
- Ultra-fast bootstrap replicates (minimum 1000). IQ-TREE v1 used -bb.
- -T, --threads _n_|AUTO
- Number of CPU threads, or AUTO to auto-detect. IQ-TREE v1 used -nt.
- -pre _prefix_
- Output file prefix.
- -o _taxa_
- Outgroup taxa.
- -t _tree_
- Starting tree file.
- -wbt
- Write bootstrap trees.
- --bnni
- Optimize UFBoot trees by NNI on bootstrap alignment (reduces overestimation).
- -alrt _n_
- SH-like approximate likelihood ratio test.
FAQ
What is the iqtree command used for?
IQ-TREE is a phylogenetic analysis tool for maximum likelihood tree inference. It supports various substitution models, model selection, and multiple bootstrap methods. IQ-TREE is known for its speed and accuracy, implementing efficient algorithms for large-scale phylogenetic analysis. It handles DNA, protein, codon, and morphological data.
How do I run a basic iqtree example?
Run `iqtree -s [alignment.fasta]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -s _file_ do in iqtree?
Input alignment file.