RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations. The RapidNJ method was originally presented in:

Rapid Neighbour Joining. Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen. In Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122, Springer Verlag, October 2008. doi:10.1007/978-3-540-87361-7_10

• Version: 2.3.2
• Added: May, 2025
• Link: https://github.com/johnlees/rapidnj

See versions which are available:

$ module avail rapidnj

Load one version into your environment and run it:

$ module load rapidnj/2.3.2
$ rapidnj

Notes from the sysadmin during installation:

$ cd /var/scratch
$ git clone https://github.com/johnlees/rapidnj.git -b v2.3.2
$ cd rapidnj
$ make
$ sudo mkdir -p /export/apps/rapidnj/2.3.2/bin
$ sudo cp -r bin/rapidnj /export/apps/rapidnj/2.3.2/bin
$ sudo chown -R root:root /export/apps/rapidnj/2.3.2

Note: the source code is old and does not compile on newer GCC. I had to compile this on CentOS Stream 8 with GCC 8.5.