CAI codon adaptation index using custom codon usage file emboss cai -seqall $input1 -outfile $out_file1 -cfile $input2 -auto On query Codon Usage File .. class:: warningmark The input dataset needs to be sequences. ----- You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai_custom.html