[R] RAxML using R

Luigi Marongiu marongiu.luigi at gmail.com
Mon Dec 29 15:23:16 CET 2014

Dear Rui,
thanks for the reply. I tried it but there were serious problems with 
the function itself: I can't use it as is because there were different 
error messages according to the parameters passed to it.
Such function has to be re-written on purpose or I should call the RAxML 
function from Linux Shell with some kind of interface.
Best regards

On 29/12/14 11:18, Rui Barradas wrote:
> Hello,
> You can put the code of that function in a separate file, say 
> "raxml.R" and then use source("raxml.R"). See the help page ?source.
> Hope this helps,
> Rui Barradas
> Em 28-12-2014 23:09, Luigi Marongiu escreveu:
>> 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
>> Luigi
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