Sneato is an extention of VGJ, which was developed by some very clever students at Auburn University. They very kindly distribute the source code under the GNU General Public License on their web site.
Here is a screenshot of Sneato immediately after starting:
PrerequisitesSneato requires the Java Runtime Environment. This is installed by default on most modern computers. If it is not installed, you can get it by going to http://www.java.com, choosing "Free Download" and following the instructions.
Downloading SneatoDownload the latest version of Sneato (v. 2) by clicking here: Sneato_v_2.zip.
Installing Sneato1. Unpack the Sneato zip file by double clicking on it.
2. Double click on the Sneato icon to start the program.
To start an analysis, click on the "Start an Analysis" button and adjust the size of the window. Next, choose "Open DB File" from the File menu, and choose the file you want to analyze. This file must be in format described below.
DB File Format:
There are two kinds of lines in the DB format: comment lines and data lines. Comment lines start with the # character and are ignored. Data lines have two parts: name and sequence, and these parts are separated by a colon (:). If multiple identical lines (i.e., sequences) are found in your file, they will be drawn as nodes whose area is proportional to the sequence frequency, so you will get a graph with big circles representing common sequences and little circles representing rare sequences.Example:# This is a comment about my otter data.
# The data are faked.
# This last otter is especially interesting...
Three test datasets are available:test.db - A simple fabricated dataset.
ptc.db - Real DNA sequence data from the PTC gene, which encodes the receptor that enables some people to taste phenylthiocarbamide (Wooding 2004).
jcv_aa_types.db - Real amino acid sequence data from the JC virus, an interesting circular DNA virus with a worldwide distribution (Wooding 2001).
To infer and draw a minimum spanning tree that describes your data choose "Spring" from the "Algorithms" menu and watch the fun!.
Sneato often draws tree with nodes that are too big and too close together. To solve this problem, click on the "Scale / 2" button two or three times and choose "Spring" from the "Algorithms" menu again.
Here is a screenshot of Sneato after it has run an analysis of PTC DNA haplotypes (Wooding 2004):
The graph that appears on the screen is a minimum spanning tree that shows the relationships among your sequences. In the graph, each circle (node) represents a different sequence. The size of the circle represents the sequence's relative frequency, and the number of occurrences of each sequences is listed as "k = ..." below the corresponding circle. Each edge (connecting line) is also labeled with the number of positional differences between the two sequences.
If you don't like the appearance of your graph, you can click and drag the nodes (circles) into suitable positions. You can also add and delete nodes and edges and change their labels and properties (size, shape, color) by choosing the appropriate mode from the control panel and double clicking. A detailed discussion of this interface is provided in the VGJ Manual.
Sneato saves results in Postscript format. Postscript is a convenient format because it looks good, is easy to print, and can be imported into a number of graphics editing programs. To save your file, choose "PostScript Output" from the File menu, then choose "Save". I prefer to modify the diagram to my liking with the Adobe Illustrator program.