LDhat is a package written in the C language for the analysis of recombination rates from population genetic data. The package is available either as C source code, or as pre-compiled DOS executables. The following programs are included:
Other programs in the package can be used to generate lookup tables and summarise the output of analyses. Currently, no GUI is available, so programs are run from the command line. A pdf manual containing information about installing, running and interpreting results from the package should be read before proceeding. An example data set - fn.seq, fn.loc and fn.lk is included in the package.
C source code can be downloaded as a single tar.gz file. A makefile is included.
Precomiled DOS executables can be downloaded individually
Executables can either be run from the command line or by double-clicking the program icon from within the LDhat folder.
A number of precomputed lookup tables are available for download. Using these tables in conjunction with lkgen will speed up analyses considerably, as the calculation of 2-locus coalescent likelihoods is the most computationally intesive aspect of the core LDhat algorithms. These tables all use the same grid for 4Ner (rho), 101 points evenly spaced between 0 and 100. They differ only in the number of sequences and the value of theta per site. Note that lkgen can be used to generated lookup tables from these for smaller numbers of chromosomes, and that minor differences in theta do not appear to strongly influence the results. All files are in gzip format.
Most of the functionality of earlier versions of LDhat is maintained in the current version, with a few exceptions. Those wanting the previous version can find it on the archived web-site
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