[R] RAxML using R

Luigi Marongiu marongiu.luigi at gmail.com
Mon Dec 29 00:09:23 CET 2014

Dear all,
I would like to run RAxML for phylogenetic analysis as indicated on 
Paradis' "Analysis of phylogenetic and evolution with R" (p. 158) thus I 
tried to use the package phyloch and its function raxml(). I am using 
Linux Ubuntu 14 and I was able to successfully install RAxML on my machine.
However phyloch is not supported by CRAN and the package as provided by 
the author on http://www.christophheibl.de/Rpackages.html cannot be 
installed -- or at least I could not using the Software centre.
I found a function on http://www.christophheibl.de/raxml.R that should 
be the actual script of the function raxml(). However I do not know how 
to implement such function. Shall I just copy it into my script? But 
then I will have hundreds of lines of code that will mess with my 
script. Can I create a kind of package that I can call from my code? Or 
is there another way to send the data to the linux shell and call the 
raxml function?
Could anybody help?
Thank you

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