zmasek bosc2010 aptx

Evolutionary tree visualization and analysis with Archaeopteryx

Christian M ZmasekSanford-Burnham Medical Research

Institute, La Jolla, California, USA


Background

• Archaeopteryx is a tool for evolutionary tree visualization and analysis

• Archaeopteryx is based on ATV which was developed to display evolutionary trees with:• gene duplications

• branch length values and support values

• separate sequence and species names


Implementation and Availability pure Java (requires Java 1.5 or greater) can be used both as:

stand alone application Java Applet (with typical Applet restrictions)

Built using/part of the open source forester framework: http://www.phylosoft.org/forester/ forester contains numerous classes for tree IO, tree analysis, etc.

Website: http://www.phylosoft.org/archaeopteryx Source code: http://sourceforge.net/projects/forester-atv/


Some notable features (1/2)

• phyloXML (http://www.phyloxml.org) support:• input

• output

• display and editing of most phyloXML elements

• Support of numerous other formats: Newick, Nexus, Tree of Life XML format, NHX

• Direct access to a variety of online databases:• TreeBASE

• TreeFam

• Pfam


Some notable features (2/2)

• Display of large trees (>20,000 nodes)

• Zoom and interactive overview

• Built in tools and algorithms for analysis:• Duplication inference

• Inference of ancestral taxonomies using UniProt database

• Tree level editing (cut, copy, paste, re-root, …)


Biological study exampleExample of analysis performed using forester/phyloXML/Archaeopteryx:

Zmasek CM, Zhang Q, and Godzik A:

“Analysis of functional profiles of eukaryotic genomes reveals

strong trends related to morphological complexity”

Late Breaking Research LBR21

Tuesday, July 13: 14:15 - 14:40


http://www.phylosoft.org/archaeopteryx

zmasek bosc2010 aptx

Technology