<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
--->
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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, using the functions in the
+<strong>Calculate→Calculate tree</strong> submenu.
+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. For details
+ about each model, see the <a href="scorematrices.html">list of
+ built-in score matrices.</a></li>
+ </ul>
+ </p>
+ <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>
+<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>
git://source.jalview.org / jalview.git / blobdiff