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sdwfrost / mevr-course-2016

Molecular Epidemiology of Viruses in R
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How to call raxml? #4

Closed BEAST-Community closed 6 years ago

BEAST-Community commented 6 years ago

@sdwfrost Could you tell me how to call raxml?

sdwfrost commented 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

https://github.com/sdwfrost/kemri-phylodynamics

sdwfrost commented 6 years ago

Also, do you look at the actual course notes:

http://sdwfrost.github.io/mevr-course-2016/

Much easier to go through!

BEAST-Community commented 6 years ago

@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.