Jurg Ott, Ph.D.

Scientific Literature, Computer Programs, Data

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. 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

• GPM, a set of programs for genotype pattern mining

• User's guide to HOMOG programs

• LINKAGE programs for Windows and Linux

• User's guide to LIPED program

• 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.

• 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.

• 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.

Photos

• First Human Gene Mapping conference in New Haven, 1973, and photos of participants

• Linkage Course in Cape Town, South Africa, 1987

• Lab Warming Party 1996

• Basic Linkage Course New York 1997

• Lab members in our library, New York, September 2000 and September 2006 

• Honoring Newton Morton's 70^th birthday, September 1999, in St. Louis (980 KB)

• Linkage Analysis Workshop in Taipei, June 2000 (743 KB)

• Lab members, Founder's Hall, 2000

• Gene Mapping Course in Beijing, October 2004

• Gene Mapping Course in Seoul, Korea, hosted by Heebal Kim

• Beijing Gene Mapping course 2008

• Beijing Gene Mapping course 2010

• Some photos (9.5 MB) from our linkage course at Peking University in July of 2014

• Beijing course 2016: Everybody, teachers, and the support trio