Moving!
2011.06.02 Leave a comment
Future documentation will be on the forester-wiki.
Archaeopteryx Evolutionary Tree Visualization and Analysis Software
2011.02.08 1 Comment
forester source code is hosted by Google code at: http://code.google.com/p/forester/
To develop forester in Eclipse:
2011.01.13 Leave a comment
Archaeopteryx (version 0.960 or higher) has now the capability to display images of organisms.
To do this, it takes advantage of the “uri” sub-element of the phyloXML “taxonomy” element, for example:
<taxonomy> <id provider="uniprot">27288</id> <scientific_name>Saccharomyces castellii</scientific_name> <uri type="image">http://www.diark.org/img/species_pict/Naumovia_castellii</uri> </taxonomy>
For an example, go here
2011.01.07 Leave a comment
Archaeopteryx applets versioned 0.960 or higher allow for the display of images (for an example, see here). In many cases, the corresponding image files do not originate from the same server as the applet itself, which leads to security related exceptions in case of unsigned applets. Thus, in order to distribute Archaeopteryx applets which are allowed to display images from arbitrary servers, the applet needs to be signed by the developer/web-master. For this, the two command line tools ‘keytool’ and ‘jarsigner‘ are needed, both of which are part of the JDK.
% keytool -genkey -keystore <path/name for your keystore> -keyalg rsa -alias <alias> -keypass <key password> -storepass <store password>
keytool will then request the following information:
% jarsigner -keystore <path/name for your keystore> -storepass <store password> -keypass <key password> -verbose archaeopteryx_applets.jar <alias>
2010.12.20 Leave a comment
The reason for the absence in the applets of the functionality found in the “File” and “Analysis” menus of the Archaeopteryx application are the security restrictions that are imposed on unsigned applets — for example, unsigned applets are not allowed to access the user’s file system and they are not allowed to print.
More information is available here.
Most the functions in the “Analysis” menu require to load an additional species tree, again something which unsigned applets are not allowed to do.
At this point I unfortunately do not have the resources to develop a “workaround” for these issues.
2010.04.19 4 Comments
08 FEB 2011: FORESTER SOURCE CODE IS NOW HOSTED BY GOOGLE CODE AT http://code.google.com/p/forester/ THUS THE MATERIAL BELOW DOES NOT APPLY ANYMORE!
Mainly for those interested in developing/modifying Archaeopteryx and its underlying forester libraries.
This describes how to import forester into the Eclipse (Java) IDE:
You will probably get two errors, to resolve them:
two errors should be gone now.
Project can now be tested by:
Project can now be built by (using Ant from within Eclipse):
2009.12.17 Leave a comment
confadd is a simple command line tool to calculate typed confidence values for a given evolutionary tree.
Its input is typically one evolutionary tree which might or might not already have confidence values associated with its branches (the ‘target’) and a set (in the range of hundreds or more) of evolutionary trees (the ‘evaluators’) in which the frequency of splits represent confidences for the ‘target’. The ‘evaluators’ are typically the result of a bootstrap re-sampling analysis or of a Bayesian method.
See: http://www.phylosoft.org/forester/applications/confadd/
2009.11.25 Leave a comment
If you are getting a ‘java.lang.NoClassDefFoundError’ you most likely forgot the ‘-cp’ (classpath) option or the file forester.jar cannot be found where your ‘-cp’ points.
If you are in the same directory as the forester.jar you need to type:
% java -cp forester.jar org.forester.archaeopteryx.Archaeopteryx
If you are in a different directory than the jar file (the usual case), it is:
% java -cp /path/to/forester.jar org.forester.archaeopteryx.Archaeopteryx
In Windows, you need to use \ instead of /.
If you want to use a configuration file (example), you need to add:
-c path/to/_aptx_configuration_file
2009.11.24 Leave a comment
In order to colorize subtrees/branches according to their associated taxonomies, the Archaeopteryx software needs to “know” two things:
In practice, the first information comes from the phyloXML formatted tree file, the second from a configuration file.
To colorize branches and (‘species specific’) subtrees according to their taxonomies:
1. Create a configuration file (see: http://www.phylosoft.org/forester/download/_aptx_configuration_file) containing lines like these:
species_color: NEMVE 0x00FFFF species_color: MOUSE 0x9620F0
Colors need to be encoded in RGB hexadecimal format (more information). For example, red would be ‘0xFF0000’, green ‘0x00FF00’.
2. Your tree file needs to be in phyloXML format (see: phyloXML) and contain matching taxonomy information (relative to the configuration file). The following elements are used for taxonomy colorization (in this order: taxonomy code (e.g. ‘NEMVE” for the sea anemone Nematostella vectensis), scientific name, common name. See http://phylosoft.org/forester/applications/phyloxml_converter/ on how to transform Newick/New Hampshire formatted tree files into phyloXML.
3. Start Archaeopteryx with the following console command:
java -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx -c path\to\_aptx_configuration_file
Needless to say, it is much more convenient to use a .bat file (Windows) or a link (Unix/Linux) instead of typing into a console each time Archaeopteryx is to be started.
4. On the Archaeopteryx application, check ‘Colorize Branches’ checkbox (this simply turns colored branch display on and off, it does not perform any color calculation) and execute ‘Tools’|’Taxonomy Colorize Branches’ (which will infer taxonomies for species specific subtrees).