QuickJoin

QuickJoin implements a heuristic for speeding up neighbour joining, making neighbour joining feasible for large sets of taxa. The inferred tree is identical to the tree inferred by the traditional neighbour joining method, but the heuristic will (potentially) construct the tree significantly faster.

QuickJoin is described in more detail in:

• QuickJoin—Fast Neighbour-Joining Tree Reconstruction T. Mailund and C.N.S. Pedersen, Bioinformatics, Vol. 20, No. 17, pp 3261-3262, 2004.
• Recrafting the Neighbor-Joining Method T. Mailund, G.S. Brodal, R. Fagerberg, C.N.S. Pedersen, and D. Phillips, BMC Bioinformatics 2006, 7:29. doi:10.1186/1471-2105-7-29

Usage

The QuickJoin program, qjoin reads a distance matrix in phylip format, or a multiple alignment in stockholm format, from an input file or stdin, and output the inferred tree, in newick format, to a file or stdout. Run 'qjoin --help' for more info.

If the input is a multiple alignment, bootstrapping support for each edge can be calculated.

Installation

From Source

The QuickJoin package is written in C++. It should compile on any Unix like system. To install the package, download the source code and unpack it (tar xzf quick-join-a.b.c.tar.gz, where a.b.c is the version number of quick-join), then run configure and make in the subdirectory quick-join-a.b.c created during unpacking. This creates the QuickJoin program, qjoin together with a number of test programs. To check that everything went right, run make check. If all tests pass, install the qjoin program by running make install. Read the INSTALL file for more info.

From Binary

Currently, the only binary distributions are Debian and RPM packages.

Contact

Thomas Mailund, <mailund@birc.au.dk>, Bioinformatics Research Center, University of Aarhus.