Linux command
raxml 命令
文本
复制后可按需替换文件名、目录或参数。
常用示例
Basic phylogenetic analysis
raxml -s [alignment.phy] -n [output_name] -m GTRGAMMA
Rapid bootstrap analysis
raxml -f a -s [alignment.phy] -n [run] -m GTRGAMMA -x [12345] -N [100]
Parsimony starting tree
raxml -y -s [alignment.phy] -n [parsimony] -m GTRGAMMA
Multiple threads
raxmlHPC-PTHREADS -T [4] -s [alignment.phy] -n [run] -m GTRGAMMA
说明
RAxML (Randomized Axelerated Maximum Likelihood) infers phylogenetic trees using maximum likelihood. It's widely used in evolutionary biology for large-scale phylogenetic analyses.
参数
- -s _file_
- Alignment file (PHYLIP format).
- -n _name_
- Output file name.
- -m _model_
- Substitution model.
- -f _algorithm_
- Algorithm to execute.
- -x _seed_
- Random seed for bootstrap.
- -N _num_
- Number of runs/bootstraps.
- -T _threads_
- Number of threads (PTHREADS version).
- -p _seed_
- Parsimony random seed.
FAQ
What is the raxml command used for?
RAxML (Randomized Axelerated Maximum Likelihood) infers phylogenetic trees using maximum likelihood. It's widely used in evolutionary biology for large-scale phylogenetic analyses.
How do I run a basic raxml example?
Run `raxml -s [alignment.phy] -n [output_name] -m GTRGAMMA` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -s _file_ do in raxml?
Alignment file (PHYLIP format).