For a full documentation, please visit the RapGreen wiki: https://github.com/SouthGreenPlatform/rap-green/wiki
You'll find there the command lines documentation of the two main entry points of the RapGreen Java package, and tutorials to install the main webservices : the tree pattern matching, and the tree viewer.
If you plan to:
-
Use RapGreen tree reconciler, in order to annote duplication and losses on a phylogenetic tree, please follow this tutorial. You could also get at look at the statistics given by RapGreen for each pair of genes of the reconciled phylogenetic tree.
-
Install the tree pattern matching service on your own data, please follow this tutorial.
-
Install the tree display service InTreeGreat this tutorial.
The general API Java documentation of the RapGreen package is available here.
RapGreen is used by several systems and platforms. Some examples are available here.
More recent version soon available
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases Jean-François Dufayard, Laurent Duret, Simon Penel, Manolo Gouy, François Rechenmann, Guy Perrière Bioinformatics, Volume 21, Issue 11, , Pages 2596–2603, https://doi.org/10.1093/bioinformatics/bti325