Mostly technical stuff with some interesting moments of life

Automate Phylogenetic Tree Coloring: Dendroscope
Dendroscope ( is a neat tool that we (SALSA group in IU) have been using in our research work related to phylogenetic trees. Recently we encountered a scenario where leaf nodes need to be colored according to a corresponding cluster number. We already had generated the mapping from leaf node labels to RGB color strings. To complicate it further, we wanted to color the “lowest single ancestor” (LSA) induced sub trees for each cluster in the same color.

Hard Labor

Open tree file using Dendroscope –> select leaf nodes for a particular cluster –> click “Select –> Advanced Selection –> LSA Induced Network” –> Ctrl+J –> check “Label Color” and “Line  Color” –> pick the desired color –> hit “close” –> click somewhere to unselect nodes/edges
Repeat this (except opening file) for each cluster.

Hard Labor with Pain Killer

You can avoid the step in bold above by having a text file with label names for the particular cluster. Then after opening the tree file you can hit Ctrl+f and specify your text file there (using the open folder icon in that). This will go through each line of the text file and select the labeled leaf nodes. This avoids having to click numerous times just to select :). Still you have to go through the pain of selecting the LSA sub tree and modifying colors.

No Pain, YES! gain

The clean way is to automate this process and Dendroscope facilitates this through its command line. Here’s what you need to generate using a simple script written by you.
open file=<path-to-your-tree-file>;select all;set edgewidth=2;set color=0 0 0;set labelcolor=0 0 0;deselect all;
find searchtext=abc;find searchtext=def
select LSA induced network;set color=r g b;set labelcolor=r g b;deselect all;
Some explanation please …
Line 1 will simply open your tree file and set all the edges to a width of 2 and everything to black
For each label in a particular cluster you need to add find searchtext=<label>; as in Line 2 (remember to separate with semi-colon)
Line 3 will select the LSA sub tree for the labels in Line 2 and line and label color to whatever color specified by r g b values
You need to include corresponding Line 2 and 3 for each cluster.
Once you generate this file simply open Dendroscope and go to “Window –> Command Input”. In the pop-up command window type source file=<path-to-your-generated-file> and hit “Apply”. That’s it enjoy!!
A good reference is available in Dendroscope’s manual at


  1. Saliya, I have a similar ask but instead of doing many things on different nodes I need to process a lot of trees, computing consensus, I was wondering if it is possible to clear the workspace in Dendroscope or not.

  2. Olga, I think this is possible with

    open file=;

    For example, if you have three files, you'll need to open issue the open command and followed by any command to compute consensus for each of them.

    1. I figured this one out and just use:
      select all;
      remove taxa=selected;

      which does the job!

    2. I guess you meant you do select all after opening all files, correct?