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New in February 2026: release of HaploGI, a program that provides haplotype data and
risk-haplotypes from sequence data in (large) pedigrees with linkage analysis results
January 2019: release of GIGI2, a faster and more efficient memory-using version of GIGI
June 2018: Release of ADMIXFRQ, GIGI-Quick
October 2017: Updated release of famSKAT-RC
August 2017: AFC (release August 1, 2017)
August 2015: PBAP (release August 7, 2015), and updated user manual;
releases of GIGI (ver 1.06.1) and GIGI-Pick (ver 1.06); release of SharedHap
- HaploGI from github
Software that implements haplotyping at sequence-level resolution in
pedigrees with a linkage-anaysis signal. Designed to work with inheritance
vector information from MORGAN. The paper that describes the approach is
Rafael A. Nafikov, Harkirat K. Sohi, Alejandro Q. Nato Jr., Andrea R. Horimoto,
Tyler R.C. Day, Thomas D. Bird, Anita L. DeStefano, Elizabeth E. Blue,
Ellen M. Wijsman (2026) Variant Prioritization by Pedigree-based Haplotyping.
Genetic Epidemiology (in press).
Nafikov et al (2026) Genetic Epidemiology, in press.
- GIGI2: a faster version of GIGI. Description of the algorithms:
"Ullah et al 2019, GIGI2: A Fast Approach for Parallel Genotype Imputation in Large Pedigrees."
bioRxiv,
Source code for GIGI2,
and the webserver version.
- ADMIXFRQ from github, or
here software implementing the approach described in Nafikov et al (2018) Analysis
of Pedigree Data in Populations with Multiple Ancestries: Strategies for Dealing with
Admixture in Caribbean Hispanic Families from the ADSP. Genetic Epidemiology
42:500-515.
- GIGI-Quick
described in Kunji K, Ullah E, Nato AQ Jr, Wijsman EM, Saad M (2018) "GIGI-Quick:
A fast approach to impute missing genotypes in genome-wide association family data".
Bioinformatics 34(9):1591-1593.
-
famSKAT-RC New release (v1.03) of famSKAT-RC, described in
Saad & Wijsman (2014) "Combining family- and population-based imputation data for association analysis of rare
and common variants in large pedigrees" Genetic Epidemiology, 38:579-590.
- AFC R code with
examples, version 1.0, released August 1, 2017.
These files replace the relationship corrected chi-square test listed below for use in the
setting of a shared control sample, and add the WQLS and famSKAT tests in the same shared
controls context.
See: Saad M and Wijsman EM (2017) Association Score Testing for Rare Variants and Binary
Traits in Family Data with Shared Controls, Briefings in Bioinformatics (published August 31 online).
- PBAP,
Version 1.0 released August 7, 2015, with
updated User Manual.
See: Nato AQ Jr, Chapman NH, Sohi HK, Nguyen HD, Brkanac Z, Wijsman EM (2015) PBAP: a pipeline
for file processing and quality control of pedigree data with dense genetic
markers. Bioinformatics 31(23):3790-3798).
- SharedHap
Released Jan. 14, 2015.
Software that implements the haplotype-sharing visualization approach described by Kim et al (2014)
Visualization of haplotype sharing patterns in pedigree samples. Human Heredity 78:1-8.
- initial release of famSKAT-RC,
Released July 25, 2014.
R scripts, to carry out a combined rare- and common-variant gene-based test of association
in the presence of related individuals, and
Ped_Pop as tarred,gzipped file ,
or Ped_Pop as a zipped file,
a C program for combining genotype imputation from GIGI and Beagle, or other pairs of genotype
imputation approaches that are based on pedigree and population-based methods.
For details of either method, see the paper: Saad and Wijsman (2014)
"Combining family- and population-based imutation data for association analysis of rare
and common variants in large pedigrees" Genetic Epidemiology, 38:579-590.
-
GIGI-Check,
Revision 1.06 released February 2, 2015.
Detection of Mendelian consistent genotyping errors in dense SNP markers in pedigrees.
See: Cheung, CYK., Thompson, E.A., Wijsman, E.M. (2014)
Detection of Mendelian Consistent Genotyping Errors in Pedigrees.
Genetic Epidemiology 38(4):291-299.
(ver. 1.0 Released Apr. 25, 2014).
-
GIGI-Pick
Revision 1.06 released February 2, 2015.
Selection of ideal subjects in pedigrees to sequence.
See: Cheung CYK, Blue EM, Wijsman EM (2014)
A statistical choice to quide sequencing choices in pedigrees.
American Journal of Human Genetics 94(2):257-267.
(ver. 0.9 Released Apr. 25, 2014).
-
GIGI:
Revision 1.06.1 released January 31, 2015.
Genotype imputation for dense markers in (large) pedigrees. See:
Cheung CYK, Thompson EA, Wijsman EM (2013) GIGI: An approach to effective imputation of
dense genotypes on large pedigrees. American Journal of Human Genetics 92:504-516.
(ver. 1.06 released Jan. 14, 2015; ver 1.05 released Aug. 16, 2014; ver 1.04 released Nov. 15, 2013; ver 1.03 released July 19, 2013; ver 1.02 released Mar. 6, 2013)
-
lnkg2lmlnk, released Mar. 12, 2012. A new converter from Linkage-style to Morgan
ver 3 style data files with some example data files
here.
- plotIBD, Released Nov. 18, 2011. A perl script
to assist with plotting sampled inheritance vectors in pedigrees, as
described in Marchani EE, Wijsman EM (2011) Estimation and visualization of
identity-by-descent within pedigrees simplifies interpretation of complex trait
analysis. Human Heredity 72(4):289-297.
- Relationship
corrected chi-square testing
and README file:.
This release (Apr. 2, 2010) replaces the version of the kinship estimation program and ancillary
programs released Nov. 12, 2009.
- Kinship
and README file:
Released Nov. 12, 2009. Software to carry
out computations to estimate kinship coefficients for case-control
analyses in the presence of cryptic relatedness, as described in the
paper: Choi et al (2009) "Case-control association testing in the presence
of unknown relationships" Genetic Epidemiology (2009), 35:668-678, PMID: 19333967
-
PANGAEA for the MORGAN package or Loki
- lnkg2lmm.
Released Sept. 1, 2007. A Perl script to convert
linkage-style files to MORGAN-lm_markers-style files, also distributed from the
PANGAEA/MORGAN distribution site.
Two sets of example files include
a binary trait,
and a quantitative
trait , both based on a couple of simulated data sets from the paper by Wijsman et al (2006)
AJHG 79:846-858.
-
Loki: Perl scripts for Loki; and two versions of Loki:
Loki ver. 2.4.5,
Loki ver. 2.4.7.
Perl scripts were released Sept. 1, 2007:
additional useful scripts for manipulating files from Loki are provided
as-is. These are scripts that members of my group have written and that
carry out commonly-used tasks. These scripts include computation of
Bayes Factors for linkage by uniform intervals or by inter-marker
intervals (different from the L-score distributed with Loki); flipping
of QTL models to eliminate the model bimodality that is
intrinsic in the analysis approach; extracting QTL models that meet particular
conditions; and extracting QTL models that fall in an ellipse in a
heterozygote-homozygote effect scatter plot. See beginning of each perl
script for program documentation. Note that the assumption behind these scripts
is that you are using Loki ver 2.4.5, 2.4.6, or 2.4.7.
-
SimSuite Ver. 1.0 Scripts,
README file, and
Examples:
Released Mar. 15, 2009. A suite of Perl scripts to manage trait simulation from Loki
output files, marker simulation, and analysis of results with Loki and/or SOLAR,
described by Igo & Wijsman (2008) Empirical significance values for linkage
analysis: trait simulation using posterior model distributions from MCMC
oligogenic segregation analysis. Genetic Epidemiology 32:119-131.
-
Simulated data used in the paper by Wijsman et al (2006) AJHG 79:846-858
is available as the "SIMULATED TEST DATA" on
the PANGAEA distribution site.
- Other programs are currently distributed informally, and in a state
that is "as is". Contact me if you are interested.