easyLINKAGE-Plus--automated linkage analyses using large-scale SNP data | Zendy

Katrin Hoffmann | Zendy; Tom H. Lindner | Zendy

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easyLINKAGE-Plus--automated linkage analyses using large-scale SNP data

Author(s) -

Katrin Hoffmann,

Tom H. Lindner

Publication year - 2005

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti571

Subject(s) - centimorgan , linkage (software) , computer science , microsatellite , mendelian inheritance , snp , genetic linkage , spurious relationship , genetics , computational biology , biology , allele , single nucleotide polymorphism , gene mapping , chromosome , machine learning , gene , genotype

We extended the original easyLINKAGE program by enabling linkage analyses for large-scale SNP data in addition to those of microsatellites. We implemented new modules for Allegro, Merlin, SimWalk, GeneHunter Imprinting, GeneHunter TwoLocus, SuperLink and extended FastSLink by automatic loop breaking and new outputs. We added conditional linkage analyses as well as multipoint simulation studies, and extended error test routines by checking for Mendelian/non-Mendelian genotyping errors and for deviations from Hardy-Weinberg equilibrium. Data can be analyzed in sets of markers, in defined centimorgan intervals and by using different allele frequency algorithms. The outputs consist of genome-wide as well as chromosomal postscript plots of LOD scores, NPL scores, P-values and other parameters.

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