Suite of PhylogEnetiC Tools for Reticulate Evolution (SPECTRE)
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.. image:: images/spectre.png
    :scale: 50%

SPECTRE a suite of tools for inferring evolutionary patterns associated with Reticulate Evolution that primarily either
create or use split systems (a collection of bipartitions of the taxa) representable in two dimensions, such as SuperQ,
FlatNJ, NetME and several NeighborNet variants.  SPECTRE provides a graphical interface to both drive and visualise the output.
The viewer allows the user to pan, zoom, rotate and modify the network, making the split networks easier to assess and interpret.
All tools in SPECTRE also have command line interfaces enabling their use within pipelines, and on servers and other high
performance computing environments.

SPECTRE's source code is written primarily in Java and is freely available under the
`GNU GPLv3 license <https://www.gnu.org/licenses/gpl-3.0.en.html>`_ via `github <https://github.com/maplesond/spectre>`_.
In addition our core data structures, algorithms and IO routines available as a library via `Maven <https://mvnrepository.com/artifact/uk.ac.uea.cmp.spectre/core>`_,
should user's which to easily leverage our code in their own projects.


.. toctree::
    :numbered:
    :maxdepth: 3

    installation
    running
    tools
    developing
    resources
    citing
    credits
    issues
    availability