Last updated 23 Nov 2022

Jurg Ott, Ph.D.

Professor Emeritus
Laboratory of Statistical Genetics
Rockefeller University, 1230 York Avenue, New York, NY 10065-6399
Tel +1 212 327 7991 ~~~ ott at

Main Research Interests

~ click for current local times in New York and China ~

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.

  • Publications, 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.

  • Flow 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 and Linux

  • 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.  

  • The maxstat 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 [2012] Hum Hered 74, 45-50)

  • The p2s program for converting files from plink to sumstat format.

  • The PAWE program was developed by Dr. Derek Gordon and may be found at his website.

  • 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 program

  • 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 analysis

  • sumstat programs (Set association analysis, Hoh et al, Genome Res 11, 2115-2119, 2001)

  • TDTae, family-based association analysis allowing for errors

  • User's guide to TLINKAGE programs

  • Statistical Utility programs, p-values for various distributions, HWE, contingency tables

Short Courses

A list of currently offered courses and courses offered in the past several years is available. A complete list of all courses offered by me and colleagues is here.



All about Beijing, China
My personal webpage, and facebook page
List of Jurg Ott's former and current scientific associates (students, postdocs, Assistant Professors, visitors...)
List of past Short Courses and lecture series given by Jurg Ott and his associates. A spreadsheet containing these data is also available.
Note: is no longer available
Webpage raising awareness of the dangers of alcohol addiction.