HIV Databases HIV Databases home HIV Databases home
HIV sequence database



Annotate Tree Explanation

Introduction

This tool generates an attractive phylogenetic tree with branches distinguished by color and stroke weight. Two sets of numerical parameters (continuous or discontinuous) can be utilized, one determining the branch color, and the other determining the branch thickness. These values can be any set of discrete or continuous numerical values, so that, for instance, virulence can be visualized relative to phylogeny.

The code for this tool is based on Newick utilities (see references below).

If you want a tree with branches distinguished by color, based on discrete categorization, see also Rainbow Tree.

Input

The input for this tool is a phylogenetic tree in Newick format. If you need to generate a Newick tree file from your sequences, there are many online tools available. Two such tools available on this website are:

Values for taxa

Number of data parameters
Do you want to decorate your tree based on one set of numerical values, or two? If you provide one set of values, color and weight will scale together. If you provide two sets of values, color will indicate one parameter, and stroke weight will indicate the other.

Taxon-to-numerical-value table
Paste or upload a text file containing your taxa names and a numerical value for each. See sample input for example. The file format should be .txt with tab-separated text. The names of the taxa must match exactly the sequence names in the Newick tree file.

Header for legend
Optional. The text entered will be shown on the color/weight legend for your tree.

Number of categories
The default is "automatically set", which means that the number of categories will be chosen based on the data. This calculation is performed by gnuplot. You may override this by entering a number.

Min-Max values for numerical range
The default is "automatically set", which means that these values will be assigned. You may override this by entering a number.

Number of post-decimal digits in labels
The default value is 2. If your values are very low (for example, in the range of 0.00001 - 0.01), then you may need to specify more decimal places to be shown.

Tree options

Tree type
Specify phylogram (rectangular branching pattern) or circular tree.

Tree width
Default width is 1000 units. A larger value will change the aspect ratio, resulting in a shorter, wider tree.
Use fixed scale will set a relationship between the branch lengths in the tree file in the output image. This allows different tree files to be drawn at the same scale.
Draw scale bar will show a scale bar for the branch lengths, indicating the number of substitutions per site.

Color choices
Choose the color palette that will present the branch colors. The first color will represent the lowest values, and the last color will represent the highest values.
Reverse palette option will reverse the palette, so the first color will represent the highest values, and the last color will represent the lowest values.

Line cap
This option will determine the shape of the joints where two branches meet.

Show only a subclade
This option will restrict the displayed tree to a subclade defined by two or more taxa. The resulting tree will display only those taxa that fall below the most recent common ancestor of the taxa specified; other parts of the tree will be omitted.

Branch weight scale
This number will increase the thickness of all branches. Must be a positive integer. Default=1

Relative branch weight
This number will change the scaling of the branch weights. At the default (1), the branch thicknesses scale linearly from the width of the thinnest to thickest branch.

Width of thinnest branch
The width of the thinnest branch. Must be a positive integer. Default = 1

Width of thickest branch
The width of the thickest branch. Must be a positive integer. Default = 15

References

Junier & Zdobnov 2010 [PMID 20472542].

Newick Utilities Tutorial.

last modified: Tue Apr 5 12:53 2016


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

 
Operated by Triad National Security, LLC for the U.S. Department of Energy's National Nuclear Security Administration
© Copyright Triad National Security, LLC. All Rights Reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health