Hi all,
I am using pal2nal to create codon-aware alignments for several gene loci before calculating selection pressure using codeml. I'm hoping that others here have used pal2nal in the same way and can help me figure out next steps.
I use
pal2nal.pl with the -nogap option, which removes all characters from the output file. When I remove this flag, I see alignments with gaps in the output file but I can't use them for the codeml analysis. I assume this is because every column in my alignment has atleast gap? This only occurs for 2 genes out of 10 in the same operon.
Has anyone run into this issue before? How have you dealt with it? My goal is to calculate dN/dS ratios using codeml and infer what selective pressures different genes might be under. I've attached one of the nucleotide and protein files here.
Thanks,
Janani