Casey Dunn committed f80422f

wrapped up phyutility demo

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 [doi:10.1098/rspb.2011.2301]( Lecture 11.  
 Populations and phylogenies. Reading: Baum and Smith Chapter 6.
-- Monday, April 15. 
+- Monday, April 15. An introduction to working with trees in phyutility. See 
 - Wednesday, April 17. Group presentation: Anthony Bui, Lei Ma, and Melanie 
 Berger present the paper
+Lecture: Phylogenomics. 
-- Monday, April 22. Lecture: Phylogenomics. 
+- Monday, April 22. 
 - Wednesday, April 24. Lecture: Phylogenies in time. Reading: Baum and Smith Chapter 11.


 A consensus tree is generated as follows:
     java -jar ~/bin/phyutility_2_2_4/phyutility.jar -con -t 0.5 \
-    -in siph_combined.run1.t.burned -out consensus.tre
+    -in siph_combined.run1.t.burned.sub -out consensus.tre
 ### Identify unstable taxa
-Find unstable taxa:
+The following calculates the Leaf Stability Index, as defined by 
+[Thorley and Wilkinson 1999](, for 
+each taxon:
 	java -jar ~/bin/phyutility_2_2_4/phyutility.jar -ls -in \
-	siph_combined.run1.t.burned.sub > stability.txt
+	siph_combined.run1.t.burned.sub > stability.txt
+The results are written to the `stability.txt` file. THis analysis reveals that 
+Cordagalma_cordiforme is the least stable taxa.
+### Pruning taxa
+Now that we know that Cordagalma_cordiforme is the least stable taxon, let's 
+remove it from the psoterior tree set and see what the support for the 
+relationships remaining taxa is:
+    java -jar ~/bin/phyutility_2_2_4/phyutility.jar -pr -in \
+    siph_combined.run1.t.burned.sub -out no_cordagalma.tre -names Cordagalma_cordiforme
+    java -jar ~/bin/phyutility_2_2_4/phyutility.jar -vert -in no_cordagalma.tre \
+    -out no_cordagalma.nex
+    java -jar ~/bin/phyutility_2_2_4/phyutility.jar -con -t 0.5 \
+    -in no_cordagalma.nex -out consensus_nocordo.tre
+Note that we converted the tree to nexus format before calculating the 
+consensus. This is required by phyutility in order to include support values 
+on the consensus tree.