HCV Database
HCV sequence database
 



To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.


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

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 (most frequent category in red, next in orange, etc.)
user-specified
Specify outgroup

Advanced options
Tree title
Branch thickness
Tip labels

 Show label:
categories full sequence names no label

 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

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




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