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A decent program for Linkage Analysis

Dean Flanders dean at birch.med.umn.edu
Fri Apr 28 15:11:54 EST 1995

: can anyone tell me where I can get a straightforward linkage
: program with good documentation.  I have looked at Linkage 5.1
: and Mapmaker and these do not fit either criteria

Now this is a decent question.  You are right there is a learning curve 
to these programs, however, you will experience that with any linkage 
analysis program you run.  Sorry, no warm fuzzy interfaces on any 
linkage analysis program I have ever run!  I would recommend taking Jurg 
Ott's linkage course or getting Joseph Terwilliger's book Handbook of 
Human Genetic Linkage.

: obscure, badly written programs, with wretched documentation.
: We have been using the original version of Linkage, which is
: adequate, but not up to snuff. I wonder if someone has a version
: of linkage between the 5.1 and 0.9 version (which we have).

Now this is a little irritating.  I think in the linkage community that 
the consensus is that these are extremely well-written programs, and just 
because you do not understand how to run them does not automatically make 
them "obscure, badly written programs, with wretched documentation".  Not 
to mention that people are still re-writing and improving on the 
original versions.  Yes, these programs are complicated, but so is linkage 
analysis.  You have just exhibited your naivete in this area to me and 
countless others.

I will send you a copy of the bionet.molbio.gene-linkage FAQ, which 
lists some other linkage programs.  I must admit you may find them 
"obscure, badly written programs, with wretched documentation", 
because every single one of them has a learning curve.  However, you  
could write your own programs, of course.

: Thanks for the help. Any suggestions would be greatly
: appreciated.

You're welcome.  One other suggestion, think before you post!  If you think 
I am irritated, I would hate to hear what the people who wrote these 
programs think of your post.

Have a nice day,


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