Please do not close this window as long as you want to view tree 58_B with ATV.
download nhx tree 58_B
ATV hints
| Zooming | ATV provides a nice zooming feature (x- and y-axis zooming) that allows handling trees with thousands of leafs. Related buttons/options:
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| Searching | ATV offers a search function (Search menu) that will highlight each maching node in red. E.g. you can use this functionality to find your query sequences ("Q8_"). |
| Handling huge topologies | ATV offers other options besides the zooming and search functions to cope with large trees:
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| Editing and saving a tree | ATV can be used as an point and click tree editor. If "editable" and "display editable info" are checked, you can click on a node and change the information and "write to tree". Since this is an applet version of ATV, the browser security prevents the application to access you local hard disc. But there is an easy way around this: the currently shown tree can be exported to text format, e.g. full featured NHX format, which can then be copied to a text editor and saved, by using the "View Tree as Text" menu. This way you can e.g. reduce the tree to a subtree, annotate the nodes and save it on your hard disc. |
| Tree Format | We're using the NHX (New Hampshire eXtended) tree format. The extensions of the Newick format enable you to store additional data for each node, e.g. the bootstrap value now has a real field. For details on NHX please refer to http://www.phylosoft.org/forester/NHX.html |
| Annotation | ATV fully supports NHX format. Node-wise annotation, like e.g. the species of a leaf sequence or the genus of a set of leafs assigned to the internal parent node, can be used for searching, coloring and edited. Other annotation, like e.g. EC number, GO or PFAM domain assignments can easily be integrated as well. |