<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
+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
</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
+<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
-\r
-<p><strong>External Sources for Phylogenetic Tree Construction</strong></p>\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. 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
+ 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
git://source.jalview.org / jalview.git / blobdiff