I have used the calcDivergenceFromAlign.pl script available in the RepeatMasker package, to produce an ‘align’ output file containing an alignment for each of the transposon sequences found by RepeatMasker against the consensus sequences from the TE library. Each alignment contains information of the Kimura distance.
The RepeatMasker util directory also contains a createRepeatLandscape.pl script which can create a histogram in Google charts that plots the the Kimura values for each of the transposon classes after parsing from the alignments. It requires an input in the following format:
./createRepeatLandscape.pl -div example_with_div.align -g # > ouput.html
where -div is the alignment file created from calcDivergenceFromAlign.pl
-g # is the genome size
However, how the output returns an html file which does not plot anything in google charts - no output values are created for plotting. Does anyone have any experience in using the .createRepeatLandscape.pl script? Is the alignment file the wrong input?