QuickJoinQuickJoinQuickJoin 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:
Warning! You are welcome to download and experiment with QuickJoin, but for practical use you should consider instead the RapidNJ tool, which contains an improved algorithm that performs much better than QuickJoin both in terms of CPU and RAM 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.
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.
Currently, the only binary distributions are Debian and RPM packages.
Thomas Mailund, <mailund@birc.au.dk>, Bioinformatics Research Center, University of Aarhus.
Time-stamp: "2006-01-28 18:24:00 mailund"