Wednesday 26 April 2017

Biodiverse now exports tree branch colours

Biodiverse version 2 will allow you to export the tree branch colours.  This means you can now get your tree colours to the point that you are happy with them, and export them to another program such as FigTree to generate figures for a publication.

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.

Shawn Laffan

For more details about Biodiverse, see 

For the full list of changes in the 1.99 series (leading to version 2) see (for all issues addressed or being targeted to fix for version 2, see ).

To see what else Biodiverse has been used for, see

You can also join the Biodiverse-users mailing list at

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