Hello community,
I have a problem with recalculating Kimura distance values using the calcDivergenceFromAlign.pl script provided with the repeatmasker software. I have a set of inveretbrate genomes and their Kimura distance values were initially calculated with special treatment for CpG sites. However, since the group of interest has very low or no DNA methylation I would like to recalculate Kimura distance values without special treatment for CPG sites.
According to the documentation of the calcDivergenceFromAlign.pl script, I should use the '-noCpGMod' flag and the '-a mynew.align' option to create a new *.align file with the new divergence value. However this does not modify the *.align file at all. Has anyone experienced this as well? Am I missing something?
Thank you in advance for your help!
