Quick-Join 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.
Split-Dist calculates the number of splits (edges) that differs for two trees. When you construct phylogenetic trees using slightly different methods, or from slightly different input data, the trees will not agreecompletely on the topology. When they differ, it is interesting to know where they differ, i.e. which edges can be found in both trees and which cannot.
CoaSim is a tool for simulating the coalescent process with recombination and gene conversion under the assumption of exponential population growth. It efficiently constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP and micro satellite haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on the states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.
GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position.
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.
HapCluster++ is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. HapCluster++ is a C++ implementation of the method described in the paper "Fine Mapping of Disease Genes via Haplotype Clustering" by E.R.B. Waldron, J.C. Whitaker, and D.J. Balding. Genetic Epidemiology. 30: 170–179. (2006).
SNPfile is a library and API for manipulating large SNP data sets with associated meta-data, such as marker names, marker locations, individuals' phenotypes, etc. in an I/O efficient binary file format. In its core, SNPfile assumes very little about the metadata associated with markers and individuals, but leaves this up to application program protocols.
Method published in BMC Bioinformatics
The association mapping method underlying Blossoc has now been published in BMC Bioinformatics, as:
Whole genome association mapping by incompatibilities and local perfect phylogenies
T. Mailund, S. Besenbacher, and M.H. Schierup
BMC Bioinformatics 2006 7(454). doi:10.1186/1471-2105-7-454.
GeneRecon in Bioinformatics
An applicaition note on GeneRecon:
GeneRecon—A coalescent based tool for fine-scale association mapping
T. Mailund, M.H. Schierup, C.N.S. Pedersen, J.N. Madsen, J. Hein, and L. Schauser
has been accepted at Bioinformatics. Advanced access at: doi:10.1093/bioinformatics/btl153. (http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl153?ijkey=kmNWzzwxg6CdVzW&keytype=ref).