+\exercise{Trees}
+{\label{treeex}
+{\sl Ensure that you have at least 1G memory available in Jalview.
+(Start with link:
+\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G},
+or in the table in the Development section of the Jalview web site
+(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds}), go
+to ``latest official build'' row and in the ``Webstart'' column, click
+on ``2G''.)}
+
+\exstep{Open the alignment at
+\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
+
+\exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
+window and a dialogue box opens. In the tree section select Neighbour
+Joining, in the drop-down list select BLOSUM62 and click the Calculate
+button. A tree window will open.}
+
+\exstep{Click on the
+tree window, a cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour.
+Place the cursor to give about 4 groups.}
+
+
+\exstep{In the tree window, select {\sl View $\Rightarrow$ Sort Alignment
+by Tree}. The sequences are reordered to match the order in the tree and groups
+ are formed implicitly. Alternatively in the alignment window, select
+{\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$
+ Neighbour Joining Tree using BLOSUM62 from...}.}
+
+\exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
+window. In the dialogue box, select Average Distance and in the drop down
+list select BLOSUM62. Click the Calculate button and a new
+tree window will appear. The group colouring makes it easy to see the differences between the two
+trees calculated by the different methods.}
+
+\exstep{In the alignment window, select sequence 2 from
+column 60 to sequence 12 and column 123. Select {\sl Calculate $\Rightarrow$
+Tree or PCA..}. , in the dialogue box select Neighbour Joining and
+BLOSUM62, then click the Calculate button.
+ A tree will appear containing 11 sequences. It has been coloured
+ according to the already selected groups from the first tree and is calculated purely from the residues
+ in the selection.}
+
+Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the
+alignment for the calculation of trees.
+
+{\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
+
+}