Closed BEAST-Community closed 6 years ago
In R? You'd use system.call
, or if you're running an RMarkdown document in RStudio, you can execute shell commands rather easily. You may also be interested in some smaller, but more up to date courses:
https://github.com/sdwfrost/mevr-course-ghana/blob/gh-pages/index.ipynb
Also, do you look at the actual course notes:
http://sdwfrost.github.io/mevr-course-2016/
Much easier to go through!
@sdwfrost In your R Markdown: https://github.com/sdwfrost/mevr-course-2016/blob/master/ml/raxml.Rmd: myalignment.rax.gtr <- raxml (myalignment, m="GTRGAMMAIX", # model f="a", # best tree and bootstrap p=1234, # random number seed x=2345, # random seed for rapid bootstrapping N=100, # number of bootstrap replicates file="ray2000", # name of output files exec="raxmlHPC-PTHREADS-SSE3", # name of executable threads=2 ) Can the above code aotumate call "raxmlHPC-PTHREADS-SSE3" or I have to put "raxmlHPC-PTHREADS-SSE3.exe" in the respective file, thanks.
@sdwfrost Could you tell me how to call raxml?