How to define an outgroup to build a robust amino acid tree I building a robust amino acid phylogeny with adequate robustness support (see previous post here).
This is a brief summary of what I have done:

I performed a BLASTp analysis using a protein sequence from species A as query against the full NCBI protein database,
downloaded all the hits in fasta format and I added the sequences I identified with the query sequence in my target genome, which is closely related to species A.
I then aligned the sequences using the Compute - Alignment - MUSCLE option in Seqotron and I saved my alignment file in Phylip format.
I tried to run this command line in RAxML to build a robust maximum likelihood tree:

raxmlHPC -m PROTGAMMAILG -n output.tre -o outgroup-p 10000 -s ~/Desktop/alignment_file.phy
However, the program showed the following error:
Error, the outgroup name &quot;outgroup-p&quot; you specified can not be found in the alignment, exiting ....
Question how can I build an outgroup for my phylogenetic tree, and how do I include it in my alignment?
I appreciate your help and suggestions!
I think you have a bug

raxmlHPC -m PROTGAMMAILG -n output.tre -o outgroup -p 10000 -s /Users)/username/Desktop/alignment_file.phy


Try the above, where username is your username. I'll check my codes later. The most important bit is the space between the -p and word outgroup. You can omit the -p 10000 it is only needed  for very geeky maximum likelihood and sets the random number stream.