-<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, using the functions in the\r
-<strong>Calculate→Calculate tree</strong> submenu. There are\r
-four different calculations, using one of two distance measures and\r
-constructing the 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>A newly calculated tree will be displayed in a new <a\r
-href="../calculations/treeviewer.html">tree viewing window</a>. In\r
-addition, a new entry with the same tree viewer window name will be added in the Sort\r
-menu so that the alignment can be reordered to reflect the ordering of\r
-the leafs of the tree. If the tree was calculated on a selected region\r
-of the alignment, then the title of the tree view will reflect this.</p>\r
-\r
-<p><strong>External Sources for Phylogenetic Trees</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. Jalview\r
- can read <a\r
- href="http://evolution.genetics.washington.edu/phylip/newick_doc.html">Newick</a>\r
- format tree files using the 'Load Associated Tree' entry of the\r
- alignment's File menu. Sequences in the alignment will be\r
- automatically associated to nodes in the\r
- </p>\r
-\r
-\r
-</body>\r
-</html>\r
+<html>
+<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. 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>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 / commitdiff