Dear Rostam,
I'll try to illustrate how to color with a small example. You could try (something like) the following:
yourtree = phytreeread('pf00002.tree')
This will generate a yourtree from one of MATLABs build-in trees. Now you want to handle the graphical elements of your tree:
h = plot(yourtree,'Type','square')
Inspect h in your workspace. This will give you a bit of a feeling how yourtree looks like.
Now you can set certain properties (such as color), for example by using:
set(h.BranchLines,'Color',[1 0 0])
This will set the color of your branch lines to red.
In a similar way, you can select other elements of yourtree and adjust its properties. I do not know what exactly you are trying to color, but I suggest you have a look at the following documentation pages as well:
Have fun!
