Crohn's Disease -- An application for SNP data.

The R script (ex_crohn.r) demonstrates the settings for SNP data set, runs the phyclust() by two clusters, calculates distances, builds a neighbor-joining tree, and applies the plotnj() to draw the tree by the HAMMING distance. The data set has 1102 SNP sequences in 8 loci, and 39 sequences are unique. In the following,

1. The data set is available in phyclust and original from Hugot, J.P., et al. (2001).

2. The left plot draws the leaf edges in a standard scale, and clusters are showed in colors but only the unique sequences are clear.

3. The right plot draws the leaf edges in a larger scale, and the duplicated sequences are condensed to the unique sequences.

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