FlatNJ (FlatNetJoining) is a program for computing split networks that allow for interior vertices to be labelled while being (almost) planar. The program takes quartet-like data as input (a so-called quadruple system that can be estimated, for example, by the program GenQS --- see below) and generates a split network following an agglomerative approach similar to the one used in methods such as NeighborJoining  and NeighborNet  (see  for details). The resulting network can then be filtered using the approach described in  . The actual drawing of the network is generated by applying the method presented in  . The network is stored in a file in nexus format. It can be displayed by any split network viewer such as those in the program SplitsTree  or the SPECTRE suite .
GenQS (Generator of Quadruple Systems) is a complementary program that computes quadruple systems directly from sequence data, geographic coordinates or split systems. The input to the program should be provided as a block of suitable type within a file in nexus format. In case of multiple sequence alignments also files in fasta format are accepted.
If you use FlatNJ please cite:
M. Balvočiūtė, M. A. Spillner, and V. Moulton. FlatNJ: A novel network-based approach to visualize evolutionary and biogeographical relationships, Systematic Biology, 2014, 63(3), 383-96.
The current versions of the programs FlatNJ and GenQS are now available as part of the SPECTRE suite. For more information on how to download, install and use the programs refer to the SPECTRE web page.
 M. Balvočiūtė, M., A. Spillner, and V. Moulton. FlatNJ: A novel network-based approach to visualize evolutionary and biogeographical relationships, Systematic Biology, 2014, 63(3), 383-96.
 S. Bastkowski, D. Mapleson, A. Spillner, T. Wu, M. Balvočiūtė, and V. Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. 2017. Submitted.
 D. Bryant and V. Moulton. NeighborNet: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol, 21, 255-65, 2004.
 S. Grünewald, K. Forslund, A. Dress, and V. Moulton. QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. Mol Biol Evol, 24, 532-38, 2007.
 D. Huson and D. Bryant. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol, 23, 254-67, 2006.
 N. Saitou and M. Nei. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 4, 406-25, 1987.
 A. Spillner, B. Nguyen, and V. Moulton. Constructing and drawing regular planar split networks. IEEE/ACM Trans Comput Biol Bioinform, 9, 395-407, 2011.