I am using Allegro 2.0 for multipoint linkage analysis using 33 bit pedigree and with 80 SNPs. It ends with "Internal error".

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Kazima Bulayeva

Hello Saeed, I'm using ,amy years for linkage analysing already many years Simwalk2 software. Simwalk2 is excellent tool for extended pedigrees with numerous inbred loops as I have from Dagestan genetic isolates (Caucasus, Russia). There is a SNP linkage option but I did not yet uset, working with genome scanned STRs. Any questions about -are welcome. Best wishes!

Saeed Ahmad

Thanks alot Kazima for the nice suggesion. I am to try the Simwalk2.

There are non-parametric and parametric linkage analyses options, IBD, Haplotypes etc...it is free and can be downloaded from Eric Sobel site at UCLA

Ellen M Wijsman

Simwalk2 works very well for STRs, but in a fairly extensive set of tests we did in 2006 (Am J Hum Genet 79:846-858, 2006), it did not perform at all well with dense SNPs.