In the format of the Rockefeller list of genetic analysis software.
PANGAEA
full name:
Pedigree Analysis for Genetics
(and Epidemiological Attributes)
version:
Last updated: December 2000.
descriptions:
Collection of ten packages for Genetic Analysis;
The new IBD packages: 2011.
The orginal four: BOREL, HARDY, MORGAN (now 2 and 3) and Pedpack
Plus: InSegT, Loki, MCLEEPS, Pedfiddler, and Eclipse
authors:
Many authors -- see individual packages.
Managed by E.A. Thompson (Univ Washington,
eathomp@u.washington.edu).
operating systems: UNIX (Compaq, Solaris, and others), Linux.
MORGAN 3
full name:
Monte Carlo Genetic Analysis
version:
Version 3.4, December 2017
descriptions:
Programs for segregation and linkage analysis, using
a variety of Markov chain Monte Carlo (MCMC) methods.
Includes MCMC methods for multilocus gene identity
by descent, and methods for simulating and inferring IBD
in population samples.
authors:
For MORGAN 3.4:
Elizabeth Thompson
eathomp@u.washington.edu), Steven Lewis
slewis@u.washington.edu.
(Some prototypes of the subprograms of ibd_create were written
by Chris Glazner and Fiona Grimson.)
For other authors of MORGAN programs :
see the MORGAN 2 information
operating systems: Linux
Possibly also UNIX (Compaq-Alpha, Solaris and others),
and Windows, via Cygwin, or using MinGW.
A fuly updated MORGAN 3.4
version of tutorial materials with compatible MORGAN 3.4 examples
references:
See the MORGAN 2 information.
The IBD packages
full name:
Identity by Descent Analysis
version:
Versions 1.0 and 2.0, 2010-2013
descriptions:
IBD_Haplo: programs for inference of IBD from population haplotypes
and genotypes. (Now integrated in MORGAN 3.)
IBDhaploRtools V1.5: an R-package for analysis of IBD_Haplo output.
Version 1.5 is on CRAN.
IBDgraph: A package for managing and resolving the output of the
MORGAN-3 gl_auto program output. (Now integrated in MORGAN 3.)
IBD Create: Programs to generate identity by descent, and haplotypes
at varying levels of LD.
authors:
For IBD_Haplo: Elizabeth Thompson, Steven Lewis and Chris Glazner.
For IBDhaploRtools V1.5: Marshall Brown (V1.0); Fiona Grimson (V1.5).
For IBDgraph: Hoyt Koepke and Lucas Kopke.
For IBD_Create: Chris Glazner (V1.0), Fiona Grimson (V2.0)
descriptions:
Programs for segregation and linkage analysis, using
a variety of Markov chain Monte Carlo (MCMC) methods.
Includes MCMC methods for multilocus gene identity
by descent and Monte
Carlo Lod scores. Also, other programs for EM analysis of
quantitative traits.
MORGAN 2.9 cleans code and fixes known problems in 2.8.3 (March 2008)
MORGAN 2.8.3 improves over 2.8.2 (Apr 2007) and 2.8.1 (Apr 2006)
MORGAN 2.8.1 supplements 2.8 (Feb 2006)
MORGAN 2.8 replaces MORGAN 2.7 (August 2005),
MORGAN 2.7 replaces MORGAN 2.6 (June 2004),
MORGAN 2.5 (November 2002) which
replaced MORGAN 2.4 (February 2002).
MORGAN 2.4 superceded MORGAN 2.3 (April 2001),
MORGAN 2.2 (April 2000) and
MORGAN 1.1.2 (July 1999)
A fuly updated MORGAN 2.9
version of tutorial materials and examples
authors:
For MORGAN 2.9
Elizabeth Thompson
eathomp@u.washington.edu)
Other authors of MORGAN programs include:
S. Basu,
A. W. George, C.J.Geyer, S. Guo, S.C.Heath, M. Jewett,
Michael Li, S. Lewis, S. Lin, N.A.Sheehan, G.Snow, W.C.L. Stewart,
and L. Tong.
Tutorial materials by M. Jewett, E.A.Thompson, A. Mitchell, A.Q.Fu,
Tia Lerud, Marshall Brown, Adam Gustafson.
operating systems: Linux (RedHat/Fedora, Ubuntu, Mandriva)
and UNIX (Compaq-Alpha, Solaris),
Windows, via Cygwin, or using MinGW. Max OSX:
Mac and Win 32 executables.
references:
E. A. Thompson (1995)
Monte Carlo in Genetic Analysis.
Technical report No. 294, Department of Statistics, University of
Washington.
E. A. Thompson (2000)
Statistical Inferences from Genetic Data on Pedigrees
NSF-CBMS Regional Conference Series in Probability and Statistics. Volume 6.
IMS, Beachwood, OH.
Thompson, E. A. (2005)
MCMC in the Analysis of Genetic Data on Pedigrees.
In
Markov Chain Monte Carlo: Innovations and Applications.
Pp. 183--216.
F. Liang, J-S Wang, and W. Kendall (eds).
Lecture Note Series of the IMS, National University of Singapore.
World Scientific Co Pte Ltd, Singapore.
Loki
version:
2.4.5 (March, 2003)
descriptions:
Program for analyses a quantitative trait observed on large pedigrees
using Markov chain Monte Carlo multipoint linkage and segregation
analysis. The trait may be determined by multiple loci.
authors:
Simon C. Heath (Univ Washington)
(now at CNG, Paris, France )
heath@cng.fr)
references:
A. W. Thomas,
Pedpack: Users' Manual.
Technical report No. 99, Dept Statistics, University of Washington.
A. W. Thomas,
Pedpack: Managers' Manual.
Technical report No. 100, Dept Statistics, University of Washington.
C. J. Geyer, (1988) Software for calculating gene survival and
multigene descent probabilities, and for pedigree manipulation and
drawing.
Technical report No. 153, Dept Statistics, University of Washington.
Pedfiddler
full name:
Pedfiddler
version:
0.6 September 2008
descriptions:
This suite of seven programs can be used as a stand-alone extension of
the pedigree drawing facilities found in
the publicly available version of
Pedpack.
operating systems: Version 0.5 tested on Unix
(AlphaLinux, Linux, OSF1, and Solaris 2.7).
Windows version tested on Windows XP Home (Should work on all win32
platforms: Win 95 and better).
Mac OSX Universal Binary tested under Mac OS 10.5 Leopard.
Eclipse
full name:
Error correcting likelihoods in pedigree structure estimation.
version:
1.1 (12/22/2003)
descriptions:
A set of three programs, preproc, eclipse2 and eclipse3 which
analyze genetic marker data for genotypic errors and pedigree errors.
Using a single preprocessing program (preproc), eclipse2 analyzes data
on pairs of individuals, and eclipse3 analyzes data jointly on trios.
PostScript and pdf documentation files are included.
authors:
Solveig Sieberts (
sieberts@u.washington.edu)
Version 0.1 was based on some earlier prototype routines by Jochen Kumm.