Description

Loki is a linkage analysis package, primarily for large and complex pedigrees, which uses Markov chain Monte Carlo (MCMC) techniques to avoid many of the computational problems that prevent exact computational methods being used for large pedigrees. Loki was originally designed for linkage analysis of quantitative traits, though there is some limited support for qualitative trait linkage analysis. The other supported analysis performed by Loki is the estimation of IBD relationship matrices for use with variance component programs such as SOLAR, which is also installed on Helix.

Loki was developed by Simon C. Heath at the Universities of Edinburgh and Washington

Version

2.4.7_4

How to Use

1. Login to Helix Systems.

2. go to the directory which contains the files need for loki to run, then type:

% loki parameterfilename logfilename

Documentation

On helix/biowulf, make sure you have Xwindows connection, then type:

% gs /usr/local/loki/docs/loki_doc.ps