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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
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--->
-<head><title>Tree Calculation</title></head>
+ * 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</strong><br>The sum of BLOSUM62 scores for the
-residue pair at each aligned position.
-</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>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>
-<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.
+ </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>
git://source.jalview.org / jalview.git / blobdiff