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1.1 Overview of MORGAN

MORGAN (Monte Carlo Genetic Analysis) is a collection of programs and libraries developed at the University of Washington under the PANGAEA (Pedigree Analysis for Genetics and Epidemiological Attributes) umbrella. This software implements a number of methods for the analysis of data observed on members of a pedigree, with the main programs implementing MCMC methods. As of the date of this tutorial, the latest MORGAN version is 2.6 which was released in February 2004. It is available for download through the MORGAN V2.6 home page at the Department of Statistics, University of Washington.

The MORGAN programs are grouped into four categories:

  1. Programs using deterministic algorithms: pedcheck checks for errors in pedigree structure and data format, see Checking Pedigree Validity. kin computes kinship and inbreeding coefficients for members of the pedigree, see Computing Kinship and One- or Two-Locus Inbreeding Coefficients.

  2. Programs using simple Monte Carlo techniques (by dropping genes down the pedigree): genedrop simulates data on a pedigree for analysis by other programs, see Simulating Data on Pedigrees. ibddrop estimates gene ibd (identity by descent) probabilities in the absence of data by Monte Carlo, see Estimating a priori IBD Probabilities by Monte Carlo.

  3. Programs using Markov chain Monte Carlo (MCMC) techniques: lm_auto end lm_pval estimate posterior gene ibd probabilities, see Estimating Posterior IBD Probabilities by MCMC. lm_lods, lm_markers and lm_bayes estimate multilocus LOD scores, see Estimating Location LOD Scores by MCMC.

  4. Programs using EM algorithm for segregation analysis with quantitative traits: includes univar, unibig, bivar and multivar, see Polygenic Modeling of Quantitative Traits by EM Algorithm.

This tutorial is based on the computing notes of Dr. Elizabeth Thompson. Descriptions of the parameter statements are taken from the `README_userdoc' files written by Myrna Jewett. The original version of this document was written in 2002 by Michael Na Li, and is now revised by Myrna Jewett.

Combined with hands-on examples, this tutorial gives a brief introduction to the usage of the main MORGAN programs. For further information, please refer to the MORGAN documentation.


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