CoAnnealing

CoAnnealing is a tool for inferring the local phylogeny (coalescent tree) at a point in a genomic region, based on haplotype sequence data. It deals with recombination events by factoring out all possible positions of recombination and search for the most likely using a simulated annealing algorithm.

CoAnnealing is developed in collaboration between Bioinformatics ApS and Bioinformatics Research Center (BiRC) and released under the GNU General Public License.

CoAnnealing is written in C++ and Guile Scheme and is available as source code (under the GNU General Public License, GPL) and as binary versions as Linux RPM files. The source code has been successfully compiled on various Linux and UNIX systems, under OS X and under Windows with Cygwin. As I have only limited access to architectures other than Linux, it is not possible for me to make binary distributions for other platforms, but if anyone is willing to build the distributions I will be more than happy to put them on this site.

The most recent versions can be downloaded below, older versions are available from here.

Binary Distributions

• coannealing-0.1.0-1.i386.rpm (alpha release)

The rpm-files were built on Linux Fedora Core 4, but should run on any i386 system.

Source Code Distributions

• coannealing-0.1.0.tar.gz (alpha release)

To build the source files, first uncompress and untar the file, then run 'configure' and finally 'make'. To test that the build was successful, run 'make check'. To install the program, run 'make install'.

    $ tar zxf coannealing-version.tar.gz
    $ cd coannealing-version
    $ ./configure
    $ make
    $ make check
    $ make install

CoAnnealing is started from the command-line; the input data and parameters for the analysis are described in one or more configuration scripts written in the Scheme programming language. Starting CoAnnealing with the configuration script input.scm is done as:

    $ coannealing input.scm

Run coannealing --help to get a complete list of command-line options accepted by CoAnnealing.

For bug-reports or feature requests, please use our bug-tracking software.

For comments or questions, please contact Thomas Mailund <mailund@birc.au.dk>, Bioinformatics Research Center (BiRC), University of Aarhus, Høegh-Guldbergsgade 10, DK-8000 Århus C.