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
To develop forester in Eclipse:
2011.01.13 Leave a comment
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!
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.