ape 3.0.7 on Mac OSX 10.8 has some problems reading fasta files! read.dna doesn’t see “G” (???) and line endings are messed up.
From the internet (http://comments.gmane.org/gmane.comp.lang.r.phylo/2509):
Feb 6, 2013
“Hi Rupert, The Mac version of ape on CRAN is not correct and has a few bugs particularly in read.dna(). Another problem is that “G” is not read (but “g” is). This does not affect the Windows version nor the sources. A solution for Mac users is re-install from the sources. Another one is to use the code of read.dna() from a previous release of ape. I’m waiting for other tests and feed-back before releasing ape 3.0-8 (within one or two weeks).
Solution: install from source:
1. Install Xcode (from Mac App store, running OSX 10.8.2)
2. In Xcode, under “Preferences”, “Downloads”, select “Command Line Tools” install button
3. Still need gfortran, go to http://hpc.sourceforge.net/ and download http://prdownloads.sourceforge.net/hpc/gfortran-mlion.tar.gz?download (for Mountain Lion only).
In Terminal, cd to the Download folder:
sudo tar -xvf gfortran-mlion.tar -C /.
4. In R Installer, select CRAN (sources) and install ape 3.0.8
5. It works!