Instructions
The tree viewer allows you to explore trees interactively, zooming in on
sections of interest, and to view additional information associated with the
sequences used to create the tree. Begin by choosing a Blocks family or
submitting your own tree.
Controls on the tree display:
- Green Rectangle at node
- Draws a new tree, with the selected node as the new root, and excludes all entries below the selected node.
- Blue Rectangle at node
- Draws the selected subtree in a new window.
- Red Box around entry name
- Links to the SwissProt record for the selected entry.
Rectangles are filled if the bootstrap value for that node is greater than 75%
Other options below tree display:
- View this tree with branch lengths turned [off or on]
- Redraws the current tree in the current window with different parameters.
- Newick formatted tree file
- Download the tree file for the currently displayed tree.
- Run Block Maker on these sequences
- Loads the Block Maker
program to make blocks from the sequences in the currently displayed tree.
- View FASTA file of the sequences
- Displays a FASTA file on the sequences contained in the currently displayed
tree.
- View extracted subclade Blocks
- Displays the currently selected Blocks family, but with all entries not in
the currently displayed tree removed. The resulting Blocks are reweighted. With
the new Blocks, you can run a MAST
search to find similar sequences or run CODEHOP
to make PCR primers.
- Blocks Family
- The ID of a Blocks family for which the tree should be displayed.
- Graphics Format
- PNG should be used as long as it works with your browser, since the images
created are higher quality and smaller. Only use JPEG if PNG doesn't work.
- Use Branch Lengths
- If this is set to yes, branch length information in the tree will be used
when drawing the tree. If the tree does not contain complete branch length
information, or this is set to no, the tree will be drawn with each branch the
same length. This can be significantly faster for a large tree.
- User-supplied Newick Tree
- If you want to view a tree of your own creation instead of one from the
Blocks database, paste it in here in Newick
tree format and leave the "Blocks Family" field blank.
- User-supplied Blocks
- Sequences in Blocks in FASTA format
- If you want to use run Blockmaker on a subtree, extract subclade Blocks, or view a FASTA file of a subtree using a tree not from the Blocks database, you must submit the Blocks and sequences in these fields.
Last modifed January 15, 2003 by N. Taylor.