A major question in genetic epidemiology nowadays is to find the genes involved in complex disease susceptibility and among those genes, to localize the variant sites explaining this susceptibility. Numerous haplotypic methods have been developped, but when the number of haplotypes is large, a grouping may be required so that the power of these analysis is not too low. Phylogenetic trees allow such groupings of haplotypes based on their evolutionary history and may help in the detection and localization of disease susceptibility sites.

ALTree is a software which performs two phylogeny-based analysis:

• it tests the association between a candidate gene and a disease
• it pinpoints markers (SNPs) that are putative disease susceptibility loci

ALTree consists is three independent programs.

ALTree

the main program which performs the association and localization test

ALTree-convert and ALTree-add-S

two utilities which help the user managing its data file before running ALTree

The method implemented in ALTree hase been fully described in Bardel et al, BMC Genet 6:24, 2005