I am trying to carry out selection analyses on a gene family to look for evidence of positive selection. I plan to do this by comparing branch models in paml to see if gene clades with duplications are under selection. I am having some trouble with paml. My tree file is in newick format and the MSA file was created by pal2nal and is in paml format. I am getting the error message: Seq #20 occurs more than once in the tree This always occurs for the 20th sequence in the MSA file (although it is not true, seq 20 does not appear twice in the tree). If I swap the order of the sequences in the alignment file is still says seq 20. Any ideas why this might be happening?