.. _credits:

Credits
=======

The paper for spectre is currently being prepared.  If you use spectre in your work and wish to publish in the meantime
please refer the project's web page: https://github.com/maplesond/spectre.git

Additionally, spectre consists on a number of tools that have already been published, if your work uses any of these
pre-published tools please also cite the associated publication(s).  A reverse chronological list of all publications
related to tools now built into spectre are in the table below.

FlatNJ
                Monika Balvociute, Andreas Spillner and Vincent Moulton, 2014.
                FlatNJ: A novel network-based approach to visualize evolutionary and biogeographical relationships.
                Systematic Biology.

SuperQ
                Stefan Grunewald, Andreas Spillner, Sarah Bastkowski, Anja Bogershausen and Vincent Moulton, 2013.
                SuperQ: computing supernetworks from quartets.
                EE/ACM Transactions on Computational Biology and Bioinformatics.

NetME
                Sarah Bastkowski, Andreas Spillner and Vincent Moulton, 2013.
                Fishing for minimum evolution trees with Neighbor-Nets.
                Information Processing Letters.

NetMake
                Dan Levy and Lior Pachter, 2010.
                The Neighbor-Net Algorithm.
                Advances in Applied Mathematics.

QNet
                Stefan Grünewald, Kristoffer Forslund, Andreas Dress and Vincent Moulton, 2006
                QNet: An Agglomerative Method for the Construction of Phylogenetic Networks from Weighted Quartets
                Molecular Biology and Evolution Volume 24, Issue 2


SPECTRE is an international collaboration.  Active contributors to spectre are listed in the following table
(in publication order):

+--------------------------+--------------------------------+-----------------------------------+-----------------------------------------------------------------------------+
| Name                     | Email                          | Current Institute                 | Contribution                                                                |
+==========================+================================+===================================+=============================================================================+
| Daniel Mapleson          | daniel.mapleson@earlham.ac.uk  | Earlham Institute (EI)            | General software development, testing, optimisation and codebase management |
+--------------------------+--------------------------------+-----------------------------------+-----------------------------------------------------------------------------+
| Sarah Bastkowski         | sarah.bastkowski@earlham.ac.uk | Earlham Institute (EI)            | SuperQ, NetMake, NetME, NeighborNet Implementation, Algorithms, Optimisers  |
+--------------------------+--------------------------------+-----------------------------------+-----------------------------------------------------------------------------+
| Monica Balvociute        | ???                            | University of Otago               | FlatNJ, NetView                                                             |
+--------------------------+--------------------------------+-----------------------------------+-----------------------------------------------------------------------------+
| Andreas Spilner          | anspillner@gmail.com           | NA                                | Mathematics, Algorithms, Optimisers, SPECTRE development                    |
+--------------------------+--------------------------------+-----------------------------------+-----------------------------------------------------------------------------+
| Taoyang Wu               | taoyang.wu@gmail.com           | University of East Anglia (UEA)   | Mathematics, Testing                                                        |
+--------------------------+--------------------------------+-----------------------------------+-----------------------------------------------------------------------------+
| Vincent Moulton          | vincent.moulton@cmp.uea.ac.uk  | University of East Anglia (UEA)   | Mathematics, Algorithms                                                     |
+--------------------------+--------------------------------+-----------------------------------+-----------------------------------------------------------------------------+


In addition, the people that contributed to the original tools which are now contained within spectre are listed in the following
table (in alphabetical order):

+-------------------------------+----------------------------------------+
| Name                          | Contribution                           |
+===============================+========================================+
| Anja Boegershausen            | SuperQ                                 |
+-------------------------------+----------------------------------------+
| Kristoffer Forslund           | QNet                                   |
+-------------------------------+----------------------------------------+
| Stephan Gruenewald            | QNet, SuperQ                           |
+-------------------------------+----------------------------------------+