Blossoc 1.1.1 review

Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input,

License: GPL (GNU General Public License) File size: 127K Developer: Thomas Mailund

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Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input, score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation.

Building the local genealogy trees is based on a number of heuristics that are not guaranteed to build true trees, but have the advantage over more sophisticated methods of being extremely fast. Blossoc can therefore handle much larger data sets than more sophisticated tools, but at the cost of sacrificing some accuracy.

Installation:

Blossoc is written in C++ 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. 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.

Usage:

Blossoc is started from the command-line and takes, as input, a file containing the positions of markers and a file containing haplotype data.

The format of the haplotype file is: One line per haplotype, where a haplotype is represented as a list of space-separated alleles, and each allele represented as either a '0' or a '1'.

The first column is a 'pseudo'-allele used for the case/control dichotomy: a '0' in the first column is taken to mean that the haplotype is a control haplotype and a '1' at the first column is taken to mean that the haplotype is a case haplotype.

Run blossoc --help to get a complete list of command-line options accepted by Blossoc.

What's New in This Release:
This version adds some algorithmic speedups to the permutation testing.