Tree Calculation

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=946037848b64fdf0a0c8ad4100753cabf0a777c1;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=e9a09085574336e1082922dbbdc7595741e6f96a;hpb=1693646e78fb0dddebcd94f8bef7e2acd3bdaae0;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index e9a0908..9460378 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -1,28 +1,85 @@ - - - -

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.
-

- - + + +Tree Calculation + +

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. +Once calculated, trees are displayed in a new tree viewing window. 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 : +

PID
The percentage identity between the two +sequences at each aligned position.
- PID = Number of equivalent +aligned non-gap symbols * 100 / Smallest number of non-gap positions +in either of both sequences
  This is essentially the 'number of +identical bases (or residues) per 100 base pairs (or residues)'.
+
BLOSUM62
The sum of BLOSUM62 scores for the +residue pair at each aligned position. +

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. +

UPGMA tree
+ UPGMA stands for Unweighted Pair-Group Method using Arithmetic + averages. Clusters are iteratively formed and extended by finding a + non-member sequence with the lowest average dissimilarity over the + cluster members. +
+
Neighbour Joining tree
+ First described in 1987 by Saitou and Nei, this method applies a + greedy algorithm to find the tree with the shortest branch + lengths.
+ This method, as implemented in Jalview, is considerably more + expensive than UPGMA. +

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 tree, by matching Sequence + IDs to the tree's leaf names. +

+ + + +