2 <head><title>Tree Calculation</title></head>
4 <p><strong>Calculation of trees from alignments</strong></p>
5 <p>Trees are calculated on either the complete alignment, or just the
6 currently selected group of sequences, using the functions in the
7 <strong>Calculate→Calculate tree</strong> submenu.
8 Once calculated, trees are displayed in a new <a
9 href="../calculations/treeviewer.html">tree viewing window</a>. There are
10 four different calculations, using one of two distance measures and
11 constructing the tree from one of two algorithms :
13 <p><strong>Distance Measures</strong></p>
14 <p>Trees are calculated on the basis of a measure of similarity
15 between each pair of sequences in the alignment :
17 <li><strong>PID</strong><br>The percentage identity between the two
18 sequences at each aligned position.<ul><li>PID = Number of equivalent
19 aligned non-gap symbols * 100 / Smallest number of non-gap positions
20 in either of both sequences<br><em>This is essentially the 'number of
21 identical bases (or residues) per 100 base pairs (or residues)'.</em></li></ul>
22 <li><strong>BLOSUM62</strong><br>The sum of BLOSUM62 scores for the
23 residue pair at each aligned position.
26 <p><strong>Tree Construction Methods</strong></p>
27 <p>Jalview currently supports two kinds of agglomerative clustering
28 methods. These are not intended to substitute for rigorous
29 phylogenetic tree construction, and may fail on very large alignments.
31 <li><strong>UPGMA tree</strong><br>
32 UPGMA stands for Unweighted Pair-Group Method using Arithmetic
33 averages. Clusters are iteratively formed and extended by finding a
34 non-member sequence with the lowest average dissimilarity over the
38 <li><strong>Neighbour Joining tree</strong><br>
39 First described in 1987 by Saitou and Nei, this method applies a
40 greedy algorithm to find the tree with the shortest branch
42 This method, as implemented in Jalview, is considerably more
47 <p>A newly calculated tree will be displayed in a new <a
48 href="../calculations/treeviewer.html">tree viewing window</a>. In
49 addition, a new entry with the same tree viewer window name will be added in the Sort
50 menu so that the alignment can be reordered to reflect the ordering of
51 the leafs of the tree. If the tree was calculated on a selected region
52 of the alignment, then the title of the tree view will reflect this.</p>
54 <p><strong>External Sources for Phylogenetic Trees</strong></p>
55 <p>A number of programs exist for the reliable construction of
56 phylogenetic trees, which can cope with large numbers of sequences,
57 use better distance methods and can perform bootstrapping. Jalview
59 href="http://evolution.genetics.washington.edu/phylip/newick_doc.html">Newick</a>
60 format tree files using the 'Load Associated Tree' entry of the
61 alignment's File menu. Sequences in the alignment will be
62 automatically associated to nodes in the tree, by matching Sequence
63 IDs to the tree's leaf names.