PANGAEA Pedigree Analysis for Genetics (and Epidemiological Attributes) PANGAEA currently consists of five packages, MORGAN (2 versions), LOKI, BOREL, Pedpack, and HARDY. WARNING: OLDER VERSIONS OF TAR MAY HAVE DIFFICULTY un-tarring these files, which were created with the DEC Alpha tar. MORGAN_V2.0.1: (released, Presidents' Day 1998) ============= Improved version of MORGAN_V2.0, with some very minor corrections, more complete documentation, and a better set of gold-standard test outputs. MORGAN_V2.0: (released Thanksgiving, Nov 1997) ============ A core of the new MORGAN with improved user interface. Only four library directories are included in Libsource_tar.Z, and Makefiles, README files, one main program directory (PolyEM), and test data and output, in Doc_Progs_etc_tar.Z MORGAN_V1.1: (released 4 July, 1997) =========== This directory contains a basic version of the gibbs programs. This version is similar to that described in the 1993 documentation. Recent modifications to convert all code to ANSI standard, and to use prototypes, may have temporarily reduced portability. The curent versions run on a DEC alpha, using cc. They are not guaranteed to run elsewhere. This version, newly installed, July 1997 has again been updated, but changes have been minor, for most programs. The programs are tar-ed in larger chunks, as detailed below, in response to requests from overseas ftp-ers. 1 tar file of Headers and library source codes: Libsource_tar includes directories Headers, Rans, Nghds, Quant, CMF, and McLib 3 tar files of main program directories; PolMix_tar includes directories PolyEM and MIXED AutoPBG_tar includes directories Autozyg and PBGibbs MulPnt_tar includes directory Multi_Pnt and its subdirectories (Multi_Pnt has been integrated to use the current libraries for this release. Other main program directories including Age_onset will be included in future releases.) 1 tar file of test data directories; Data_tar (Note: not all the data used for testing can be made freely available --- some files that may be referred to in some current Makefiles have been removed from these data directories. ) LOKI Version 2.1.4 (released St Patrick's Day, March 1998) ================== A slightly updated version of LOKI Version 2.1.3 (released St David's Day, March 1998) which was a slightly updated version of LOKI Version 2.1 (released Christmas, Dec 1997) Monte Carlo analysis of multiple QTL ==================================== In subdirectory, LOKI_V2.1 is a tar file of of the package LOKI developed by Simon C. Heath. LOKI analyses a quantative trait observed on large pedigrees using Markov chain Monte Carlo multipoint linkage and segregation analysis. The trait may be determined by multiple loci. The package is based on work originally done at University of Edinburgh, UK, and developed at University of Washington under NIH grant GM-46255, Genetic Epidemiology of Complex Traits. The package is newly released (December, 1997). The directory contains a single tar file. After downloading and extracting, consult the README file in the directory created which provides instructions for installing the program, using the Makefile. Documentation is in the subdirectory docs. Questions may be addressed to Simon Heath (heath@linkage.rockefeller.edu). A bug report file was added, Jan 9, 1998. BOREL ===== Programs for the Inference of Relationships from Genetic Data sibships_95: A set of C programs, test inputs, and test outputs, to compare sibship hypotheses among a set of individuals. For further information, please contact Dr. Ian Painter (ian@statgen.ncsu.edu) sibdocum.ps: PostScript file of documentation for the above programs estiprogs_96: Some C programs for computing exclusion probabilities, finding possible parents and parent pairs, estimating pairwise relationships, and finding parental (single and pair) likelihoods. These are updated versions of old programs (1986 and earlier) by Elizabeth Thompson, resulting from work with Dr. T. R. Meagher. They have recently been updated, and modified to allow computations for X-linked loci, in the context of projects with Dr R. Frankham (MacQuarie U.) and Dr Paulo Prodohl (U. Georgia). They are still under development, and are NOT either efficient or user-friendly. These programs handle genotypic data only -- a couple used to handle phenotypic data, but this is NOT guaranteed. Pedpack ======= This is NOT the full Pedpack package previously distributed by Dr. Alun Thomas. The version here is based on an earlier version of Pedpack, developed by Dr. Thomas at the University of Washington, and extended by several others, in particular Dr. Charles J. Geyer. The package is distributed here primarily for its interactive pedigree graphics capabilities. Included are routines to input the pedigree in Pedpack format, and routines for constructing and improving a graphical representation, for editing the graph interactively, and producing a PostScript output file. Most of these routines are described in Technical Report #153 (C. J. Geyer, (1988), "Software for calculating gene survival and multigene descent probabilities, and for pedigree manipulation and drawing"). For further information read also the instructions in the readme_drawped file in the Pedpack directory. Subdirectories are included as single tar files; Xxxx_tar should be extracted to create a directory Xxxx. HARDY ===== Program and documentation by Dr. Sunwei Guo, for MC estimation of P-values in a sparse two-dimensional contingency table, or for Hardy Weinberg equilibrium. The reference is Guo and Thompson (1992, Biometrics). In case of questions about the program, please contact Dr. Guo (guo_s@epivax.epi.umn.edu).