What software does one use to make lexical network graphs? I am thinking of the nice tree dimensional graphs that have both splits and linkages. What is the software used and what is the best structure of the database? I attach some examples of graphs of the type I want to make.
Use graphviz. You specify your graph in terms of nodes and edges. If you really want splits, treat them as a node but give them a distinct shape.
Graphviz is just great for this, because it does all the layouting for you. Just google "graphviz download". It is software that originated from ATT's Bell labs and is used by very many researchers worldwide. (as you can hear, I'm a fan)
SplitsTree http://www.splitstree.org/ (Huson 1998, Huson & Bryant 2006, 2015) is a good choice since it was specially developed for the generation of unrooted phenogram networks, featuring the NeighborNet algorithm (Bryant & Moulton 2004) for computing relative distance between comparative matrix values.* If your matrix is formatted correctly and rendered as a distance network instead of a similarity network, results are computed instantly and can be exported (among other formats) as a pdf that preserves a high resolution vector graphic of the tree, useful for formatting further in a paper.
To get started, point the program to a tab separated text file version of your matrix with left headings only and ensure that the first line begins with two spaces followed by the total number of cases or varieties you are comparing (i.e., the total number of rows that follow). Methodologies are clarified and elaborated further (and with far more sophisticated discussion) in the online manual; but IMO the example sets included with the installation are especially useful for getting started.
*Thanks to Ken Manson for introducing me to this software and methodology in 2007.
References
Bryant, David & Vincent Moulton. 2004. Neighbor-Net: An agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution 21(2). 255–265. DOI: 10.1093/molbev/msh018
Huson, Daniel H. 1998. SplitsTree: A program for analyzing and visualizing evolutionary data. Bioinformatics 14(10). 68–73. DOI: 10.1093/bioinformatics/14.1.68
Huson, Daniel H. & David Bryant. 2006. Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution 23(2). 254–267.
Huson, Daniel H. & David Bryant. 2015. SplitsTree4, version 4.14.5. Downloaded from http://www.splitstree.org/.
http://www.splitstree.org/
Many thanks Jamin, do you also have any literature suggestions regarding how to format a distance network correctly for language data?
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