A couple of people have asked about inputting their own integerisations. We don't allow this currently, but I have implemented a possible approach to allowing this in the branch skip_integerisation. In this workflow, required input is the usual plus a unimog file, in which each genome has one entry (i.e. the integers are defined over all the plasmids, not pairwise like in integerisation from alignment). A containment network is still built by calculating containment distances with nucmer, but for calculating DCJ-Indel distances the provided unimog is then used.
Question is: is this a reasonable way of allowing skipping, and is it worth adding it to next pling version?
A couple of people have asked about inputting their own integerisations. We don't allow this currently, but I have implemented a possible approach to allowing this in the branch
skip_integerisation. In this workflow, required input is the usual plus a unimog file, in which each genome has one entry (i.e. the integers are defined over all the plasmids, not pairwise like in integerisation from alignment). A containment network is still built by calculating containment distances with nucmer, but for calculating DCJ-Indel distances the provided unimog is then used.Question is: is this a reasonable way of allowing skipping, and is it worth adding it to next pling version?