<html>\r
-\r
+<head><title>Tree Calculation</title></head>\r
<body>\r
-tree \r
+<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
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff