for non-coding regions substitution_rates.py $input $out_file1 #if $region.type == "win": ${region.input2} ${region.input2.dbkey} ${region.input2.metadata.chromCol},$region.input2.metadata.startCol,$region.input2.metadata.endCol,$region.input2.metadata.strandCol #else: "None" #end if Alignment block Intervals in your history

.. class:: infomark **What it does** This tool takes a pairwise MAF file as input and estimates substitution rate according to Jukes-Cantor JC69 model. The 3 new columns appended to the output are explained below: - L: number of nucleotides compared - N: number of different nucleotides - p = N/L ----- .. class:: warningmark **Note** Any block/s not containing exactly two sequences, will be omitted.