Rainbow Tree

Purpose: To create a color-coded phylogenetic tree. See details below.

Details: This tool groups sequences based on sequence names, and draws a color-coded tree using up to 20 colors. It is useful when you already have a tree and want to color its branches to depict particular groupings of sequences. For example, the Sample Input with default settings depicts the HIV-1 M-group reference phylogeny color-coded by subtype.

For more information, see Rainbow Tree Explanation.

Download stand-alone R script:

• R script (For details, see Rainbow Tree Explanation.)

References

• Paradis, E. (2006) Analyses of Phylogenetics and Evolution with R. New York: Springer.
• Paradis, E., Claude, J. and Strimmer, K. (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289–290.