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