X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=47cac5b935e7107eff9c4b9c67bde4115048650a;hb=91cb798a47b512b0ac3792fd3a84f2c5bd3c7218;hp=16d7bbc5e37a0c755d174dd75b98b0779f1189e3;hpb=3396e9f33cf3a16a7f38f5163cd057df4b859e7e;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 16d7bbc..47cac5b 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -1,28 +1,62 @@
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.
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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.
+
Calculation of trees from alignments
+Trees are calculated on either the complete alignment, or just the +currently selected group of sequences, using the functions in the +Calculate→Calculate tree submenu. There are +four different calculations, using one of two distance measures and +constructing the tree from one of two algorithms :
+Distance Measures
+Trees are calculated on the basis of a measure of similarity +between each pair of sequences in the alignment : +
Tree Construction Methods
+Jalview currently supports two kinds of agglomerative clustering +methods. These are not intended to substitute for rigorous +phylogenetic tree construction, and may fail on very large alignments. +
A newly calculated tree will be displayed in a new tree viewing window. In +addition, a new entry with the same tree viewer window name will be added in the Sort +menu so that the alignment can be reordered to reflect the ordering of +the leafs of the tree. If the tree was calculated on a selected region +of the alignment, then the title of the tree view will reflect this.
+ +External Sources for Phylogenetic Trees
+A number of programs exist for the reliable construction of + phylogenetic trees, which can cope with large numbers of sequences, + use better distance methods and can perform bootstrapping. Jalview + can read Newick + format tree files using the 'Load Associated Tree' entry of the + alignment's File menu. Sequences in the alignment will be + automatically associated to nodes in the +
+ +