Pling!
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Pling is a software workflow for plasmid analysis using rearrangement distances, specifically the Double Cut and Join Indel (DCJ-Indel) distance. By intelligently combining containment distance (shared content as fraction of the smaller) and DCJ-indel distance ("how far apart evolutionarily" in a structural sense), and by preventing shared mobile elements from clouding the issue, it infers clusters of related plasmids.

.. toctree::

   installation.rst
   basic.rst
   tutorial.rst
   output.rst
   advanced.rst
   tips.rst
   citation.rst