Usage of VITESSE

Joseph D. Terwilliger joe at pigen.cpmc.columbia.edu
Wed Nov 19 15:15:10 EST 1997



On 18 Nov 1997, Alex Schaffer wrote:

> As for acceptability in print, my count suggests that over 10%
> of 1997 linkage analysis papers are using VITESSE at least for some analyses
> and some of these are in the best journals (e.g., the recent paper
> in JAMA on Alzheimer's linkage to chr. 12). 
> 
> However, it is a sad, sad state of affairs that over 50% of
> linkage analysis papers still use only LINKAGE.

No offense intended, but when I have small pedigrees or simple problems to
analyze, I would normally use regular linkage myself - it is much
easier for me to modify the code since it is written in (albeit
poorly commented) Pascal... I would say that there is not any compelling
reason to prefer fastlink or vitesse over linkage or liped when
computational time is not a big issue - which it normally is not unless
you have huge or loopy pedigrees.  Anyway it all depends on what you are
doing, but the results SHOULD be the same from whatever program you use -
linkage, liped, fastlink, mendel, vitesse, etc... The only one I know of
that gives consistently discrepant results consistently is Genehunter
because it throws away portions of the data from medium to large pedigrees
and thus does not compute the lod score from the full set of data.

Joe Terwilliger




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