menu.
<mapID target="seqfeatures" url="html/features/seqfeatures.html"/>\r
\r
<mapID target="webservice" url="html/webServices/index.html"/>\r
- <mapID target="clustal" url="html/webServices/clustal.html"/>\r
+ <mapID target="clustal" url="html/webServices/msaws.html#clustal"/>\r
+ <mapID target="muscle" url="html/webServices/msaws.html#muscle"/>\r
\r
<mapID target="io" url="html/io/index.html"/>\r
<mapID target="edit" url="html/editing/index.html"/>\r
\r
<mapID target="sorting" url="html/calculations/sorting.html"/>\r
<mapID target="trees" url="html/calculations/tree.html"/>\r
+ <mapID target="treeview" url="html/calculations/treeviewer.html"/>\r
<mapID target="pca" url="html/calculations/pca.html"/>\r
<mapID target="pairwise" url="html/calculations/pairwise.html"/>\r
<mapID target="redundancy" url="html/calculations/redundancy.html"/>\r
<tocitem text="Sequence Features" target ="seqfeatures"/>\r
</tocitem>\r
<tocitem text="Web Services" target="webservice" expand="false">\r
- <tocitem text="Clustal Alignment" target="clustal"/>\r
+ <tocitem text="Clustal Alignment" target="clustal"/>\r
+ <tocitem text="Muscle Alignment" target="muscle"/>\r
+ <tocitem text="JNet Secondary Structure Prediction" target="jnet"/>\r
</tocitem>\r
<tocitem text="Input /Output" target="io"/>\r
<tocitem text="Editing Alignment" target ="edit"/>\r
+ <tocitem text="Viewing Trees" target ="treeview"/>\r
<tocitem text="Colour Schemes" target="colours" expand="false">\r
<tocitem text="ClustalX" target="colours.clustal"/>\r
<tocitem text="Zappo" target="colours.zappo"/>\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 treeviewer window name will be added in the <a href="../calculations/sort.html">Sort\r
+menu</a> so that the alignment can be reordered to reflect the ordering of\r
+the leafs of the tree.</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
--- /dev/null
+<html>
+<head>
+<title>The Tree Viewing Window</title>
+</head>
+<body>
+<p><strong>The Tree Viewing Window</strong></p>
+<p>
+ When a tree has been calculated from an alignment, or imported via a
+ file or web service it is displayed by Jalview's tree viewing
+ window. Trees can be rearranged, used to select sequences and groups
+ in the associated alignment, saved in newick format or exported as an
+ image or postscript file.</p>
+<p>
+ Selecting sequence ids at the leaves of the tree selects the
+ corresponding sequences in the original alignment. These selections
+ are also reflected in any other analysis windows associated with the
+ alignment, such as another tree viewer.</p>
+
+<p>
+ Clicking on an internal node of the tree will rearrange the tree
+ diagram, inverting the ordering of the branches at that node.
+</p>
+<p>
+ Clicking anywhere along the extent of the tree (but not on a leaf or
+ internal node) defines a tree 'partition', by cutting every branch
+ of the tree spanning the depth where the mouse-click occured. Groups
+ are created containing sequences at the leaves of each connected
+ subtree. These groups are each given a different colour, which are
+ reflected in other windows in the same way as if the sequence ids
+ were selected, and can be edited in the same way as user defined
+ sequence groups.
+</p>
+<p>Tree partitions are useful for comparing clusterings produced by
+different methods and measures. They are also an effective way of
+identifying specific patterns of conservation and mutation
+corresponding to the overall phylogenetic structure, when combined
+with the <a href="../colourSchemes/conservation.html">conservation
+based colour scheme</a>.</p>
+<p><strong>File Menu</strong></p>
+<p>This menu allows the displayed tree to be saved as a Newick tree
+file (Save->Newick File), printed or exported as an image (PNG) or
+Postscript file.
+</p>
+<p><strong>View Menu</strong></p>
+<p>When the tree viewer is opened, it displays all the annotation
+associated with a tree. Trees calculated by Jalview have branch
+lengths, which correspond to the distance measure used to construct
+the tree. Tree imported from outside may also contain bootstrap information,
+or additional leaves from sequences not present in the associated
+alignment.
+</p>
+<p>The view menu contains options controlling the way a tree is
+rendered and labelled:</p>
+<p><ul>
+<li><strong>Fit to Window</strong><p>
+The tree layout will be scaled to fit in the display
+window. You may need to reduce the font size to minimise the leaf
+label overlap when this option is selected.
+</p></li>
+<li><strong>Font Size -</strong><em>n</em><p>
+Brings up a dialog box to set the font size for the leaf
+names. <em>n</em> is the current font size.
+</p></li>
+<li><strong>Show Distances</strong><p>
+Labels each branch or leaf with its associated branch length.
+</p></li>
+<li><strong>Show Bootstrap values</strong><p>
+Labels each branch or leaf with its associated bootstrap value.
+</p></li>
+<li><strong>Mark unlinked leaves</strong><p>
+Toggles the display of a '*' at the beginning of a leaf label to
+indicate that there is no sequence corresponding to that leaf in the associated alignment.
+</p></li>
+</ul>
+</p>
+</body>
+</html>
<html>\r
<head><title>Web Services</title></head>\r
<body>\r
-<p><strong>Web services </strong></p>\r
+<p><strong>Web services</strong></p>\r
<p>Originally Jalview used SRS server to retrieve sequence features for a given\r
alignment. In addition certain remote alignment programs could be called from\r
the Jalview interface and the results displayed in a new alignment panel. </p>\r
-<p>The main emphasis of the current development of the Jalview Project is to implement\r
- various sequence alignment programs, tree analysis, PCA algorithms on a large\r
- cluster based witihin the Barton Group. Jalview will be able to call these remote\r
- procedures without the user having to install any new software. <br>\r
- The main advantage of using these remote web services is that the computing\r
- power available is much greater than that of the users work station.</p>\r
+<p>Jalview's web based computations are now being developed further,\r
+ using SOAP based services to expose protein sequence alignment and\r
+ secondary structure prediction programs. These services actually run\r
+ on the cluster based in Dundee, and maintained by the Barton group.\r
+</p><p>In the future, Jalview will be able to discover services\r
+ dynamically, and the repertoire will include methods for repeat\r
+ analysis, sequence identification and remote homology\r
+ detection. The web service methodology will also allow potentially\r
+ expensive Jalview analysis functions like <a\r
+ href="../calculations/pca.html">PCA</a> to be distributed, if\r
+ necessary, when the user is dealing with very large numbers of sequences.</p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / commitdiff