msa seems to be just the thing I need! With this post, I hope to make it better for people that (also) start to use it.
I found the help for the msa::msa funcion (
?msa::msa) and ran the first example code:
filepath <- system.file("examples", "exampleAA.fasta", package="msa") mySeqs <- Biostrings::readAAStringSet(filepath) msa::msa(mySeqs)
The error I got was:
Error in get(as.character(FUN), mode = "function", envir = envir) : object 'msaClustalW' of mode 'function' was not found
I feel this error should be a bit more helpful, as it is from a (in this case, my first) msa example. I predict the error should be mentioning to me that I need to install ClustalW on my local computer, something like:
Error in [some function] : ClustalW not found. Tip: install ClustalW
If my prediction is correct, I hope msa will help its new users better by giving a more helpful error message.
Else, this message is a regular bug report :-)
Thanks, Richel Bilderbeek