I am trying to use mauve to compare the genome alignments I got from different softwares but I can't get it to work (every time I solve an error, a new one comes !). Do you know a way to compare all my alignments and view the common regions, rearrangements etc ?
An alternative to mauve is Trebol but it doesn't exist on linux. I can also try to make dotplots of 2 and 2 genomes but it is quite long to do.
Thank you very much for your help, Best, Sofia