RapGreen

Manipulate and annotate phylogenetic trees

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Table of Contents

• Installation
  • Using Docker
  • Using Singularity
  • Using Bioconda
• Documentation
• How to cite?

Installation

Using Docker

See details

First you must have Docker installed and running.
Secondly have look at the availabe rapgreen biocontainers at quay.io.

Then:

# get the chosen rapgreen container version
docker pull quay.io/biocontainers/rapgreen:1.0--hdfd78af_0
# use an rapgreen
docker run quay.io/biocontainers/rapgreen:1.0--hdfd78af_0 rapgreen --help

Using Singularity

See details

First you must have Singularity installed and running.
Secondly have look at the availabe rapgreen biocontainers at quay.io.

Then:

# get the chosen rapgreen container version
singularity pull docker://quay.io/biocontainers/rapgreen:1.0--hdfd78af_0
# run the container
singularity run rapgreen:1.0--hdfd78af_0

You are now in the container. You can use an RapGreen.

Using Bioconda

See details

Install rapgreen

conda install -c bioconda rapgreen

Update rapgreen

conda update rapgreen

Uninstall rapgreen

conda uninstall rapgreen  

Documentation

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.

How to cite

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