UPGMA tree
If this option is selected then all sequences are used to generate a UPGMA
tree. The pairwise distances used to cluster the sequences are the percentage
mismatch between two sequences. For a reliable phylogenetic tree I recommend
other programs (phylowin, phylip) should be used as they have the speed to use
better distance methods and bootstrapping. Again, plans are afoot for a server
to do this and to be able to read in tree files generated by other programs.
When the tree has been calculated a new window is displayed showing the tree
with labels on the leaves showing the sequence ids. The user can select the
ids with the mouse and the selected sequences will also be selected in the alignment
window and the PCA window if that analysis has been calculated.
Selecting the 'show distances' checkbox will put branch lengths on the branches. These branch lengths are the percentage mismatch between two nodes.
Neighbour Joining tree
The distances between sequences for this tree are generated in the same way
as for the UPGMA tree. The method of clustering is the neighbour joining method
which doesn't just pick the two closest leaves to cluster together but compensates
for long edges by subtracting from the distances the average distance from each
leaf to all the others.
Selection and output options are the same as for the UPGMA tree.