Scientific Literature, Program Guides
Most of the manuals below contain
links to programs for downloading. For some of the programs listed
I have newer versions that are not yet on this webpage; write to
me if you are interested. Also, I can supply 64 bit versions of
the Pascal programs. Earlier versions of our programs, and other
freely available software, is available from the ftp
site at the European Bioinformatics
Institute (EMBL-EBI), Hinxton, UK.
corrections for the 1991 and 1999
editions of Analysis of Human Genetic Linkage (see also
notes to this book), and for
Handbook of Human Genetic Linkage;
exercise files for the latter book.
Our Handbook is now available as a
pdf file after copyright has been transferred from the
original publisher to the authors. The Chinese version
of the Handbook was translated by Dr. Yi Li, Associate Professor,
Taiyuan, Shanxi, PRC (if you are unable to open this file, please
download a current version of the Adobe Reader or read it in an updated browser version).
- A very useful book, Combinatorial Algorithms For Computers and Calculators (Nijenhuis & Wilf 1978), is now freely available for download.
Genetic Analysis Software. This list was created by Dr.
Wentian Li when he was at Columbia University (1995-96). It was
then moved to Rockefeller University (1996-2002) and is now
maintained as a github repository by Dr. Gao Wang.
All of Jurg Ott's Linkage
Newsletters, published between 1987 and 1998.
chart of Jim Renwick's linkage program
User's guide to EH program
- Simple spreadsheet to compute equivalent numbers of recombinants
The FP test for genetic
case-control association studies
User's guide to HOMOG programs
LINKAGE programs for Windows
User's guide to LIPED program
Sex-specific maps of the
human chromosomes. These maps were calculated based on highly
polymorphic markers in 15 CEPH families comprising 239
individuals. Although our publications (Fann
& Ott, Genomics 29, 571-575, 1995; Li
et al, Hum Hered 48, 266-270) appeared some 20 years
ago, results still seem valuable and rare to find elsewhere. For
example, the graph below shows a fitted curve for 19 intervals on
chromosome 19, with x-axis = male map position at interval
midpoint, and y = scaled difference between female and male map
lengths in the given interval.
program for permutation (randomization) based tests in
case-control studies. A special program version, maxstatRS,
is available for analysis of Hamming distance data.
Brief description of MDSOutlier
program (Shen et al, Hum Hered 2010;70:227-231)
User's guide to NOCOM program to
analyze mixtures of distributions
The p53MH algorithm (Hoh et al,
PNAS 99, 8467-8472, 2002)
Partition test (manual, program,
and sample files) in GWAS to test a set of small p-values
versus their number under no association (Ott,
Liu, Shen  Hum
Hered 74, 45-50)
The p2s program for converting
files from plink to sumstat format.
Programs PAWE and PAWE3D.
The files for these programs were copied unmodified from our
previous server, http://linkage.rockefeller.edu, which is no
- I have been using Pseudomarker
extensively and like this sophisticated program. To avoid some of its
pitfalls I have written a shell program, runPM, around it that is described and available here.
The randompat program package
for association of genotype patterns (diplotypes) with disease
Scan statistics in gene
mapping (Hoh and Ott, PNAS 97, 9615-9617, 2000)
User's guide to SIMNUCLEAR
Documentation to SIMULATE
program for simulating large numbers of marker loci independent
of a disease locus.
Documentation to SLINK program
SNPstat program for genetic
association analysis, including conditional and interaction
sumstat programs (Set
association analysis, Hoh et al, Genome Res 11,
TDTae, family-based association
analysis allowing for errors
User's guide to TLINKAGE
Statistical Utility programs,
p-values for various distributions, HWE, contingency tables