#nexus

begin paup;

log file=paup.log start replace;
exe mydata.nex;
set crit=like;
lset userbrlens;
  
[!
**********************************************************************
*** Tree is (1,2,(3,(4,((5,8),(6,((7,9),10)))))). All 17 branch    ***
*** lengths are equal to 0.1. Assume group of interest includes    ***
*** taxa 7-10. Quantities T, I, I', and E are explained in Figure  ***
*** 1 of the paper by Lewis, L. A., and P. O. Lewis. 2005.         ***
*** Unearthing the molecular phylodiversity of desert soil green   ***
*** algae (Chlorophyta). Systematic Biology 54(6): 936-947.        ***
**********************************************************************
]
gettrees file=tree.tre storebrlens unrooted;

[!
**********************************************************************
*** Get tree length T = 1.7                                        ***
**********************************************************************
]
describe 1 / plot=none brlens=sumonly;

[!
**********************************************************************
*** Prune taxa in group of interest (7-10) to obtain I' = 1.1      ***
**********************************************************************
]
delete 7-10 / prune;
describe 1 / plot=none brlens=sumonly;

[!
**********************************************************************
*** Clear all trees, restore all taxa, and re-read the treefile    ***
**********************************************************************
]
cleartrees;
restore all;
gettrees file=tree.tre storebrlens unrooted;

[!
**********************************************************************
*** Prune taxa not in group of interest to obtain I = 0.8, the     ***
*** inclusive phylodiversity. The exclusive phylodiversity, E, can *** 
*** be obtained as follows: E = T - I' = 1.7 - 1.1 = 0.6           ***
**********************************************************************
]
delete 1-6 / prune;
describe 1 / plot=none brlens=sumonly;

log stop;

end;