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HIV sequence database



Rainbow Tree

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

Input tree
Paste your tree file
in Newick format
icon

Or upload Newick tree file

Options
Color tree according to
icon
first character(s) in sequence names
the column in field of sequence names delimited by
paste or upload grouped sequence names (example) icon

Assign colors default icon
user-specified
Specify outgroup icon

Advanced options
Tree title
Branch thickness
Tip labels

 Show label:
categories full sequence names no label symbols icon

 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 icon
Show node labels icon
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:

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

last modified: Tue May 27 11:09 2014


Questions or comments? Contact us at seq-info@lanl.gov.

 
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