RAxML outgroup seemingly not working

Question

[dthorbur]

I'm using RAxML to create gene trees. A call I use is simplified below (I've taken out the full paths, bootstraps, and seeds):

raxmlHPC -f d -m GTRGAMMA  -o LG14_Gar_ENSLOCT00000011644_ENSGACT00000016797_CDS -s All_ENSGACG00000015146_chrI_CDS_aln.fa -n All_ENSGACG00000015146_chrI_CDS

The outgroup I have specified as the sequence in the fasta file, but without the > character. The result I get is something like this:

I'm at a loss why there is neither an error message, or why the specified outgroup doesn't appear to be an outgroup. The rest of the sequences are intra-specific but from different populations, so naturally we would expect the inter-specific sequences to be the most different. Yet RAxML doesn't appear to agree with that. The sequences have been aligned with MAFFT using a codon alignment algorithm.

Any help would be greatly appreciated.