I am trying to build a robust amino acid phylogeny with adequate robustness support (see previous post: How to make a robust amino acid phylogeny with adequate robustness support).
This is a brief summary of what I have done: First, 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. Then 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 "outgroup-p" you specified can not be found in the alignment, exiting ....
So my question is: 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!