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A phylogenetic tree analysis package (species/gene tree reconciliation, tree pattern matching, Javascript interfaces ...)

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RAP-Green is a new implementation and an improvment of the RAP software (, which permits to compare gene and species trees, infers duplication events, and provide confidence score in function conservation between genes.

Afterwards, it became a development plateform, to implement several phylogenetic tree analysis softwares.

RAP-Green includes also two graphical web interfaces : one to display phylogenetic trees, explore them and annotate them ; and another to explore a tree forest, using tree pattern matching, and a tree pattern daemon implemented in the Rap-Green java package.

The whole documentation is available here using GitHub wiki.

To quickly test the software, you can visite this list of installed services.



For general questions or comments, you can contact the project owner (jeanfrancois.dufayard at


Tree pattern matching is a way to explore a large library of phylogenetic trees, extracting those which contain specific phylogenetic patterns.

Tree pattern matching facilities are in constant development. The installation of this system in your environment should be the occasion of a collaboration.

A complete service is composed with 3 modules: a web tree displayer (InTreeGreat, in the treedisplay directory), a tree pattern editor (in the treepattern directory), and a tree pattern matching daemon running in a accessible server (in the rapgreen Java package).

A tutorial to install a phylogenetic tree pattern matching service is available here using GitHub wiki


Documentation is yet to be improved.

For a command line option description: here

For a code documentation: here using HTML preview

Project was formerly supported by Helix INRIA project, and LBBE, and is now supported by the UMR AGAP (CIRAD) and project Ancestrome.