• Running Environment (for all programs): i686-pc-linux-gnu, 1030432 KB RAM, 2-CPU 2GHz and 2.4 GHz.

• Considerable changes in running time should be expected on different computers. Runs on a modern PC are at least twice faster than the reported results.

• In the experiments we used Vitesse v2.0, and Genehunter v2.1.

Experiment 1: (The pedigree topology is taken from pedigree B in Kruglyak et al., 1996, the marker data is simulated. We used both increasing number of loci and increasing number of untyped individuals.)

This is a complex inbred pedigree that occurred in the study of Werner syndrome (Thompson and Wisjman 1994). The pedigree has 15 people (with inbreeding loops). All the markers have 5-10 alleles.
 

Experiment 2:(The pedigree topology is taken from pedigree C in Kruglyak et al., 1996, the marker data is simulated. We used both increasing number of loci and increasing number of untyped individuals.)

This pedigree has 29 people (with no inbreeding loops). All the markers have 5-10 alleles.
 

 Clarifications to the tables:

***     Not Applicable - Vittese doesn't handle looped pedigrees.
*****  Over 12 hours.
#        In Genehunter, the likelihood is calculated several times, for different positions of the disease gene on the marker map.
         The number of likelihood calculations equals the number of markers in the analysis.

For the Superlink runs, in cases where there was a variance in the results, the run times of several runs are reported.

• Kruglyak L, Daly M, Reeve-Daly M, and Lander E. "Parametric and Nonparametric Linkage Analysis: A Unified Multipoint Approach."

American Journal of Human Genetics 58 (1996): 1347-1363.