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Jalview and Archeopteryx


Jalview includes basic support for phylogeny, but it could do better. Archeopteryx is a powerful java based phylogeny visualization tool associated with the Forester package - but doesn't include any support for working with alignments or character matrices.


This project would involve creating a prototype version of the Jalview Desktop that integrates Archeopteryx with Jalview's existiing alignment and PCA visualizations.


Understanding Jalview and Archeopteryx's datamodel and mapping them to allow data exchange. Understanding and adapting both application's GUI model to replace Jalview's existing tree viewer with an Archeopteryx window. Extending Jalview to take advantage of Archeopteryx's own analysis capabilities (e.g. taxon name analysis, etc,) and support for phylogenetic formats like phyloXML and NEXUS.

Involved toolkits or projects 

Java 1.7. Forester. Jalview.

Degree of difficulty and needed skills 

This is most likely a medium to difficult project. You will need to know how phylogenetic trees relate to multiple sequence alignments, and have the confidence to hack Java Swing Applications. There are lots of easy milestones in this project, but also some challenges - such as inferring taxon assignments with Archeopteryx's routined using the annotation Jalview retrieves from online databases.

Involved developer communities

Forester Jalview

What developer communities would be involved, and what are the primary communication channels (IRC, mailing lists, Twitter, etc)?

  • [JimProcter|Jim Procter]
  • [ChristianZmasek|Christian Zmasek]