problem finding tree.raxml function

[raynamharris]

Thanks for the excellent tutorial.

I think I don't quite have raxml properly installed in work with R. I downloaded it (version 8.2.12) using conda install -c bioconda raxml at the command line, but I'm getting the following error message in R. I'm using a Mac OS (10.15.7) and R version 4.1.1.

Any ideas?

> tree.raxml(folder='2.Alignments', 
+            FilePatterns= 'Masked', 
+            raxml_exec='raxmlHPC', 
+            Bootstrap=100, 
+            outgroup ="Mus_musculus")
Error in tree.raxml(folder = "2.Alignments", FilePatterns = "Masked",  : 
  could not find function "tree.raxml"
> system("raxmlHPC")

 Error, you must specify a model of substitution with the "-m" option

[cromanpa94]

My pleasure! It seems that RAxML is installed correctly. I can only think of two potential solutions:

1. If you're using RStudio, open it from the terminal: open /Applications/RStudio.app. You shouldn't have any issues when running tree.raxml from just R.
2. Based on the could not find function "tree.raxml" error, please make sure that the package is loaded. Maybe you were trying something else, re-started R/RStudio, and forgot to load it again?
   Please do let me know if you're still having issues!

[raynamharris]

Thanks! That worked. I think I needed to open from the command line and reload the package.

Alternatively, that could have been an error message that it was throwing when I tried to do this with my own selection of sequences and species for which there were too few to build a tree. Thanks!