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-<head>
-<title>Tree Calculation</title>
-</head>
-<body>
- <p>
- <strong>Calculation of trees from alignments</strong>
- </p>
- <p>
- Trees are calculated on either the complete alignment, or just the
- currently selected group of sequences, via the <a href="calculations.html">calculations dialog</a> opened from the <strong>Calculate→Calculate
- Tree or PCA...</strong> menu entry. Once calculated, trees are displayed in a new <a
- href="../calculations/treeviewer.html">tree viewing
- window</a>. There are four different calculations, using one of two
- distance measures and constructing the tree from one of two
- algorithms :
- </p>
- <p>
- <strong>Distance Measures</strong>
- </p>
- <p>Trees are calculated on the basis of a measure of similarity
- between each pair of sequences in the alignment :
- <ul>
- <li><strong>PID</strong><br>The percentage identity
- between the two sequences at each aligned position.
- <ul>
- <li>PID = Number of equivalent aligned non-gap symbols *
- 100 / Smallest number of non-gap positions in either of both
- sequences<br> <em>This is essentially the 'number of
- identical bases (or residues) per 100 base pairs (or
- residues)'.</em>
- </li>
- </ul>
- <li><strong>BLOSUM62, PAM250, DNA</strong><br />These options
- use one of the available substitution matrices to compute a sum of
- scores for the residue pairs at each aligned position.
- <ul>
- <li>For details about each model, see the <a
- href="scorematrices.html">list of built-in score
- matrices</a>.
- </li>
- </ul></li>
- <li><strong>Sequence Feature Similarity</strong><br>Trees
- are constructed from a distance matrix formed from Jaccard
- distances between sequence features observed at each column of the
- alignment.
- <ul>
- <li>Similarity at column <em>i</em> = (Total number of
- features displayed - Sum of number of features in common at <em>i</em>)
- <br />Similarities are summed over all columns and divided by
- the number of columns. <br />Since the total number of
- feature types is constant over all columns of the alignment,
- we do not scale the matrix, so tree distances can be
- interpreted as the average number of features that differ over
- all sites in the aligned region.
- </li>
-
- </ul> Distances are computed based on the currently displayed feature
- types. Sequences with similar distributions of features of the
- same type will be grouped together in trees computed with this
- metric. <em>This measure was introduced in Jalview 2.9</em></li>
- </ul>
- <p>
- <strong>Tree Construction Methods</strong>
- </p>
- <p>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.
- <ul>
- <li><strong>UPGMA tree</strong><br> 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.
- <p></p></li>
- <li><strong>Neighbour Joining tree</strong><br> First
- described in 1987 by Saitou and Nei, this method applies a greedy
- algorithm to find the tree with the shortest branch lengths.<br>
- This method, as implemented in Jalview, is considerably more
- expensive than UPGMA.</li>
- </ul>
- <p>
- A newly calculated tree will be displayed in a new <a
- href="../calculations/treeviewer.html">tree viewing
- window</a>. 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.
- </p>
-
- <p>
- <strong>External Sources for Phylogenetic Trees</strong>
- </p>
- <p>
- 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 <a
- href="http://evolution.genetics.washington.edu/phylip/newick_doc.html">Newick</a>
- 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.
- </p>
-
-
-</body>
-</html>
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