NCBI’s Tree Viewer

NCBI’s Tree Viewer


This video introduces an interactive Tree
Viewer application that uses your own data. It can generate printable vector images as
PDFs, and you can embed the viewer into web pages. Those of you familiar with our Genome
Workbench will see similarities to the Tree View function there, but this viewer can be
used independently of Genome Workbench. I’ll first demonstrate some of the basic functions
of Tree Viewer, then show you where you can find the API and documentation. Let’s begin on this page of examples, which
is available at the base NCBI URL, followed by forward slash projects, forward slash treeview. You could start by uploading your own data
using the Upload button on this page, but, I’ll begin with this Rectangular Cladogram
example. You can use this slider to zoom in and out,
or the plus and minus icons for more fine zoom control. And to scroll to a different
part of the tree, click-and-drag with your mouse. When you mouse over a node, you get a common
set of options, and you see parameters that you’ve applied to this node, such as
color. If you want to view your tree in a different
layout, choose Tools/Layout. I’ll change mine to Circular Tree. A very handy feature is the Overview mode.
Click this magnifying glass icon and a thin rectangle outlines the region that you were
viewing. Click again to return to the previous view. Also in Tools, you can save your tree in a
few formats, including a PDF file. I’ll choose Tools/Download/PDF file, then click Create
PDF-file. The resulting link, which can be shared with colleagues, and the View button,
opens a PDF view of the tree in a browser. To create a local copy, use the Save button.
I’ll just move on to my final demonstration, the Upload feature. You can upload a file in newick format, or
in asn binary or text; you can also specify a URL for either an http or ftp location,
or you can directly paste in text in newick or asn format. I’ll upload this local file
in newick format. Okay, to get to Tree Viewer documentation,
use either of these question mark icons to go to the viewer’s home page, and here under
the Table of Contents you will find the information you need to get started. We hope you find the Tree Viewer useful, and
please send all comments, questions and bug reports to this address, [email protected]

2 thoughts on “NCBI’s Tree Viewer

  • Hi…..I am using another software but the cladogram produced by your tree viewer is different from what I got through the software. Genomes were the same. A little confusing.

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