-<html>\r
-<head><title>Tree Calculation</title></head>\r
-<body>\r
-<p><strong>Calculation of trees from alignments</strong></p>\r
-<p>Trees are calculated on either the complete alignment, or just the\r
-currently selected group of sequences. There are four different\r
-calculations, using one of two distance measures and constructing the\r
-tree from one of two algorithms :\r
-</p>\r
-<p><strong>Distance Measures</strong></p>\r
-<p>Trees are calculated on the basis of a measure of similarity\r
-between each pair of sequences in the alignment :\r
-<ul>\r
-<li><strong>PID</strong><br>The percentage identity between the two\r
-sequences at each aligned position.\r
-<li><strong>BLOSUM62</strong><br>The sum of BLOSUM62 scores for the\r
-residue pair at each aligned position.\r
-</ul>\r
-</p>\r
-<p><strong>Tree Construction Methods</strong></p>\r
-<p>Jalview currently supports two kinds of agglomerative clustering\r
-methods. These are not intended to substitute for rigorous\r
-phylogenetic tree construction, and may fail on very large alignments.\r
-<ul>\r
-<li><strong>UPGMA tree</strong><br>\r
- UPGMA stands for Unweighted Pair-Group Method using Arithmetic\r
- averages. Clusters are iteratively formed and extended by finding a\r
- non-member sequence with the lowest average dissimilarity over the\r
- cluster members.\r
-<p></p>\r
-</li>\r
-<li><strong>Neighbour Joining tree</strong><br>\r
- First described in 1987 by Saitou and Nei, this method applies a\r
- greedy algorithm to find the tree with the shortest branch\r
- lengths.<br>\r
- This method, as implemented in Jalview, is considerably more\r
- expensive than UPGMA.\r
-</li>\r
-</ul>\r
-</p>\r
-<p></p>\r
-<p><strong>The Tree Viewing Window</strong></p>\r
-<p>\r
- When the tree has been calculated a window is displayed showing the\r
- tree, with the leaves labelled with sequence ids. \r
-<p>Selecting the 'show distances' checkbox will put branch lengths on the branches.\r
- These branch lengths are the percentage mismatch between two nodes. </p>\r
- \r
-<p>\r
- Selecting sequence ids at the leaves of the tree selects sequences\r
- in the original alignment. These selections are reflected in any\r
- other analysis windows open on the same alignment. </p>\r
-<p>\r
- Clicking on an internal node of the tree will rearrange the tree\r
- diagram, inverting the ordering of the branches at that node.\r
-</p>\r
-<p>\r
- Clicking anywhere along the extent of the tree (but not on a leaf or\r
- internal node) defines a tree 'partition', by cutting every branch\r
- of the tree spanning the depth where the mouse-click occured. Groups\r
- are created containing sequences at the leaves of each connected\r
- subtree. These groups are each given a different colour, which are\r
- reflected in other windows in the same way as if the sequence ids\r
- were selected, and can be edited in the same way as user defined\r
- sequence groups.\r
-</p>\r
-<p>Tree partitions are useful for comparing clusterings produced by\r
-different methods and measures. They are also an effective way of\r
-identifying specific patterns of conservation and mutation\r
-corresponding to the overall phylogenetic structure, when combined\r
-with the <a href="../colourSchemes/conservation.html">conservation\r
-based colour scheme</a>.</p>\r
-\r
-\r
-<p><strong>External Sources for Phylogenetic Tree Construction</strong></p>\r
- <p>A number of programs exist for the reliable construction of\r
- phylogenetic trees, which can cope with large numbers of sequences,\r
- use better distance methods and can perform bootstrapping. See the\r
- <a href="../webservices/phylogeny.html">Phylogenetic Web\r
- Services</a> page for directly accessible methods. It will also be\r
- possible to read trees into Jalview directly, in the near future.\r
- </p>\r
-\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * 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.
+ *
+ * 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/>.
+ * 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.
+ <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>
git://source.jalview.org / jalview.git / blobdiff