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
.. 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.