Rainbow Tree

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

Input tree

Paste your tree file in Newick format [Sample Input]
Or upload Newick tree file
Or put job number

Options

Color tree according to	first character(s) in sequence names the column in field of sequence names delimited by paste or upload grouped sequence names (example)
Assign colors	default user-specified
Specify outgroup

Advanced options

Tree title
Branch thickness	1 2 3 4
Tip labels	Show label: categories full sequence names no label symbols   paste or upload grouped sequence names for symbol tips (example)      Label style (in radial tree): axial horizontal
Legend	Style: vertical horizontal no legend  Show legend at: top left top top right left center right bottom left bottom bottom right
Color interior edges
Show node labels
E-mail	Always email results

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: This tool was developed by Peter Hraber and Hyejin Yoon, using APE in R, as described in:

• 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.