This blog post provides a few more details, as well as a video showing how to visualise and export the data. Exported data can be used in, for example, NMDS analyses to relate turnover to environmental patterns (see González-Orozco et al. 2013 and González-Orozco et al. 2014).
One thing to note is that if you have a phylogeny selected then you can view which branches of the tree are shared or differ between the index and neighbour group (cell). This is evident in the video, and is described in an earlier blog post: https://biodiverse-analysis-software.blogspot.com/2014/10/new-tree-plots-in-biodiverse.html
1. Generate the data
|If you only want to build the matrix (or matrices) then select this option.|
|Currently only delimited text is supported, but you can choose whether to use normal, sparse or GDM compatible output formats. Hovering over the options gives more details about what they do.|
For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse/
To see what Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList
You can also join the Biodiverse-users mailing list at http://groups.google.com/group/Biodiverse-users or follow the google plus page: https://plus.google.com/+BiodiverseSoftware