Tree Calculation

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=946037848b64fdf0a0c8ad4100753cabf0a777c1;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=3d62766852c3dfae2ab63751ceb0baacd6ac7f7e;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 3d62766..9460378 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -1,6 +1,85 @@ - - - -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. +

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