Hello all. I have been using Mauve to visualize genome draft assemblies compared against a reference genome. I have been reading the website on how to interpret the similarity plots that are displayed in the viewer. Specifically they say "The height of the similarity profile is calculated to be inversely proportional to the average alignment column entropy over a region of the alignment." - I understand this as a the greater the height, the more similar two sequences are (correct me if I'm wrong). However, when choosing the similarity ranges, I am having trouble understanding how to interpret this.
So it seems that when comparing similar sequences the similarity plots (purple) should be fairly high and full, like in this:
When selecting to display both the similarity plot and range my plots look like this, Similarity range lines are dark purple:
Further more, I visualized two identical sequences in mauve and got this:
So how do I interpret what the similarity plot ranges mean? What I think is that the higher a similarity range line is, the less range of differences there are between the sequences. The spiky purple shading also indicates ranges, but it seems to be more exaggerated than the dark purple line.
Also in the mauve output, what are the .backbone and .bbcols files?