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Archaeopteryx: Visualization, Analysis, and Editing of Phylogenetic Trees  

2011-09-08 09:37:04|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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Overview

Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees.
Archaeopteryx (the successor to
ATV) is entirely written in the Java programming language (it is based on the forester libraries). It can be used both as applet (ArchaeopteryxA and ArchaeopteryxE) and as a standalone application. Answers for some frequently asked questions are (will be) available here, phyloXML related issues might be discussed here.
Screenshots

species colorization and gene duplication display circular display type species images large trees (proteobacteria from NCBI taxonomy) search function protein architecture display expression value display unrooted display type multiple support values
Species colorization and gene duplication display (demo) Circular display type (demo) Species images (demo) Large trees (proteobacteria from NCBI taxonomy) Search function (demo) Protein architecture display (demo) Expression value display Unrooted display type (demo) Multiple support values (demo)



New Features
Archaeopteryx version 0.957 beta (2010.09.06):
Fixed midpoint rooting error.

Complete version history


Requirements

Archaeopteryx requires Sun Java version 5 (also called Java 1.5) or higher. Archaeopteryx applets (ArchaeopteryxA, ArchaeopteryxE) require the Sun Java plug-in. Most web browsers under Windows and Apple OS X have this already installed. Under Linux, this plug-in might need to be installed, though. For example, under Ubuntu Linux, the Sun Java plug-in can be downloaded and installed with the following command: "sudo apt-get install sun-java6-jre sun-java6-plugin". More information is available here.
Archaeopteryx has been tested on Windows, Linux, and Apple Macintosh (OS X with Java 1.5.0_13).


Download

Latest version: Archaeopteryx 0.957 beta (2010.09.06)
Jar file containing Archaeopteryx: ?
forester.jar
To download, right-click and then select "Save Link As..." (on Windows), then launch Archaeopteryx by clicking the downloaded "forester.jar" file on your own desktop.
Example configuration file: ?
_aptx_configuration_file
Jar file containing only Archaeopteryx applets (only needed for web developers): ? archaeopteryx_applets.jar
Sign up for the Archaeopteryx mailing list to be informed of new versions and changes.
Previous versions


If Archaeopteryx proves useful in your research, please consider making a donation via PayPal to ensure maintenance and future development:


Examples
ArchaeopteryxE examples (embedded applet)
Organism images (Images of various fungi and nucleariids are shown, more information is available here)
Cnidaria (Cnidarian phylogeny from the Tree of Life project with 2461 external nodes)
Mollusk taxonomy (Mollusca from the NCBI taxonomy with 5632 external nodes)
Multiple support values (Hominidae species tree)
Wnt (gene tree from TreeFam)
Apaf-1 (domain architectures)
Bcl-2 (annotated gene tree)
Apaf-1 and Bcl-2 (tabbed display)
Amphibians (Amphibian phylogeny) [same tree displayed differently]
Various display types
ArchaeopteryxE without controls and menu

ArchaeopteryxA examples (open own frame)


Usage

Answers for some frequently asked questions are (will be) available at aptxevo.


Windows, Apple Macintosh (OS X)

Clicking on the "forester.jar" file should start it, the configuration file ("_aptx_configuration_file") will be used if it is in the same directory as the jar file.


Unix, Linux, Windows, Apple Macintosh (OS X)

command line (without use of a configuration file or "_aptx_configuration_file" is in the same directory as the jar file):
"java -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx"

command line for using a configuration file anywhere in the file system:
"java -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx -c path\to\_aptx_configuration_file"


command line for directly opening a treefile and using a configuration file anywhere in the file system:
"java -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx -c path\to\_aptx_configuration_file treefile"


Increasing memory

Since the Java default memory allocation is quite small, it might by necessary (for trees with more than around 5000 external nodes) to increase the memory which Java can use, with the "-Xms" and "-Xmx" Java command line options. For example:
"java -Xms32m -Xmx256m -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx -c path\to\_aptx_configuration_file"


Windows batch file

To avoid typing, it is easiest to create at batch (.bat) file. For example create a new file named "aptx.bat" and put a line like this into it:
java -Xms32m -Xmx512m -cp "C:\path\to\forester.jar" org.forester.archaeopteryx.Archaeopteryx -c "C:\path\to\_aptx_configuration_file"
Clicking on "aptx.bat" should now start Archaeopteryx.


Archaeopteryx applets

A description about how to use Archaeopteryx as Java applet in your own website is available here.


Input and Output Formats
phyloXML – phylogenetic XML (Reference: Han M.V. and Zmasek C.M. (2009): phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10:356)
New Hampshire/Newick – produced by most major phylogenetic analysis software (e.g. PHYLIP)
NHX – New Hampshire Extended (deprecated) – our extension of the New Hampshire format
Nexus – the format used by PAUP*, MrBayes, and many others
ToL Response XML Format – the format currently used by the Tree of Life project webservices (input only)
PDF, PNG, GIF, and JPG image output
Important Note

Certain programs (e.g. MrBayes) produce New Hampshire formatted trees (possibly inside a Nexus file) where internal tree nodes have both branch length as well as support values [e.g. "(a:0.1,b:0.2)0.90:0.1"]. By default, Archaeopteryx interprets these support values (the "0.90" in the example) as node names. In most situations this is not a big problem, except if the trees are to be rerooted -- then the "support values" move to the wrong branches (because node names are attached to a node and not to a branch like support values).
To correctly interpret such internal numbers as support values, check "Internal Numbers Are Confidence Values" under the "Options" menu (in the Archaeopteryx application) before reading the tree file.


Development Snapshot

A snapshot of a more current development version (0.961 beta K48 2011.05.27) can be downloaded here (use at your own risk):
launch (using Java Web Start): // using JavaScript to get location of JNLP file relative to HTML page var dir = location.href.substring(0, location.href.lastIndexOf('/')+1); var url = "http://www.phylosoft.org/archaeopteryx/webstart/archaeopteryx_dev_webstart.jnlp"; deployJava.createWebStartLaunchButton(url, '1.6.0');
Archaeopteryx: Visualization, Analysis, and Editing of Phylogenetic Trees - 喜欢吃桃子 - wangyufeng的博客


download: ? forester_dev.jar
example configuration file: ? _aptx_configuration_file_dev


Source Code

The source code for Archaeopteryx (as application/module of the the open source forester libraries) is available on Google code: http://code.google.com/p/forester/


Mailing List

Please consider joining the Archaeopteryx mailing list to be informed of updates and changes
(probably no more than about one message per month).

Email:


Other Programs for Phylogenetic Tree Display and Analysis
Drawgram/Drawtree (PHYLIP)
Hyperbolic display for large trees:
HyperTree
Combining and visualizing evidence from different phylogenetic analyses:
TreeGraph 2
jsPhyloSVG
Treevolution
Interactive Tree Of Life:
iTOL
Python Environment for Tree Exploration:
ETE
TreeDyn
PhyloWidget
PhyloBox

Please let us know if you have a suggestion for this list.


References and Contacts

Han M.V. and Zmasek C.M. (2009). phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics, 10:356. [PubMed] [BMC Bioinformatics] [PDF]

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