Colours can be exported with the Nexus and tabular Tree formats. If you use the tabular format then there will be a column in the output table called Colour. For the Nexus format, the colours are stored in the comments block for each branch.
|Click on the "Export colours" checkbox to export the colours in a Nexus file.|
A few examples are below.
|View labels tab with a set of labels highlighted on the tree.|
|The selection colours displayed in FigTree.|
|A cluster analysis with six clusters coloured.|
|The tree in FigTree with the six clusters coloured.|
|A user defined selection.|
|The same user defined selection in FigTree.|
The colouring works for anything that is applied to the tree, so you can also export continuous palettes when you have calculations per node (branch).
|PD calculated for each cluster node (branch).|
|And the same PD colouring now in FigTree.|
Kudos to Luke Fitzpatrick for getting it working.
For more details about Biodiverse, see http://purl.org/biodiverse
For the full list of changes in the 1.99 series (leading to version 2) see https://purl.org/biodiverse/wiki/ReleaseNotes (for all issues addressed or being targeted to fix for version 2, see https://github.com/shawnlaffan/biodiverse/milestone/4 ).
To see what else Biodiverse has been used for, see https://purl.org/biodiverse/wiki/PublicationsList
You can also join the Biodiverse-users mailing list at http://groups.google.com/group/Biodiverse-users