There are multiple fixes and some new features in this version.
Utilities:
- INSTALLATION. Pling is finally installable, making it easier to run. Conda install is now also available
- Updated documentation
New features:
- Skip integerisation and use your own custom integer sequences instead - #63
- Can now run on linear genomes and regions of genomes - #44 and #6
- Optionally output Cytoscape formatted json files of network visualisations - these can be loaded directly into Cytoscape
For details on any of these please see the documentation.
Bug fixes:
- Fix #71
- Fix #57 - this fix in certain cases changes the integerisation, and the DCJ-Indel distances, but only in already quite diverged plasmid with previously high DCJ-Indel distances. Therefore this fix is unlikely to affect any clustering results. Please see the issue for a more detailed discussion.
- MAJOR fix: we have been using DCJ-Indel distances as weights in our clustering algorithm, without realising that the algorithm treats more weight as more favourable, i.e. edges with larger DCJ-Indel distances are more favourable. This is conceptually completely incorrect, and the opposite of what we would want. We have updated our plasmid network package plasnet to use the unweighted version of asynchronous label propagation. Version 0.6.0 of plasnet will be enforced as the minimal version required for pling. This change has not affected any of the smaller datasets we have previously run on (including our paper results), but does appear to affect the clustering for larger datasets (order of a 1000 and up)