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