Split networks are a type of phylogenetic network that allow visualization of 
conflict in evolutionary data. We present a new method for constructing such 
networks called FlatNetJoining (FlatNJ). A key feature of FlatNJ is that it 
produces networks that can be drawn in the plane in which labels may appear 
inside of the network. For complex data sets that involve, for example, 
non-neutral molecular markers, this can allow additional detail to be visualized 
as compared to previous methods such as split decomposition and NeighborNet. We 
illustrate the application of FlatNJ by applying it to whole HIV genome 
sequences, where recombination has taken place, fluorescent proteins in corals, 
where ancestral sequences are present, and mitochondrial DNA sequences from gall 
wasps, where biogeographical relationships are of interest. We find that the 
networks generated by FlatNJ can facilitate the study of genetic variation in 
the underlying molecular sequence data and, in particular, may help to 
investigate processes such as intra-locus recombination. FlatNJ has been 
implemented in Java and is freely available at 
www.uea.ac.uk/computing/software/flatnj.