Recently, the Earlham Institute, in the UK, released a set of software tools that are of relevance to this blog — SPECTRE. These tools are described in a forthcoming paper:
Sarah Bastkowski, Daniel Mapleson, Andreas Spillner, Taoyang Wu, Monika Balvočiūte and Vincent Moulton (2017) SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. [Now published.]
This is a toolkit rather than simple-to-use program, meaning that the various analyses exist as separate entities that can be combined in any way you like. More importantly, new analyses can be added easily, by those who want to write them, which is not the case for more commonly used programs like SplitsTree. This way, the analyses can also be incorporated into processing pipelines, rather than only being used interactively.
Apart from the usual access to data files (including Nexus, Phylip, Newick, Emboss and FastA formats), the following network analyses are currently available:
NeighborNet, NetMake, QNet, SuperQ, FlatNJ, NetMEThe program also outputs the networks, of course. Here is an example of the SPECTRE equivalent of a NeighborNet analysis from a recent blog post (where the network was produced by SplitsTree, and then colored by me).
Running the program(s) is relatively straightforward, once you get things installed. Installation packages are available for OSX, Windows and Linux.
Sadly, for me installation was tricky, because SPECTRE requires Java v.8, which is unfortunately not available for OSX 10.6 (which runs on most of my computers). Even getting Java v.8 installed on the one computer I have with a later version of OSX was not easy, because installing a Java Runtime Environment (the JRE download file) from Oracle does not update the Java -version symlinks or add Java to the software path — for this I had to install the full Java Development Kit (the JDK download file). Sometimes, I hate computers!