Sequenza is part of our pipeline, we are very happy with it ! I am in charge of implementing a phylogenetic reconstruction tool that would use Sequenza output. When looking at the segments.txt file generated by Sequenza, il looks much nosier than the red signal plotted in the chromosome plots. I really need to reduce this .txt file to a smaller, smoother one, merging blocks together. It looks like you are already implementing this in order to generate the plots, could it be possible to intercept the data that is actually used in the plots?
Thank you very much in advance, Marc