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

K Hoffmann; T H Lindner

doi:10.1093/bioinformatics/bti571

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

Bioinformatics. 2005 Sep 1;21(17):3565-7. doi: 10.1093/bioinformatics/bti571. Epub 2005 Jul 12.

Authors

K Hoffmann¹, T H Lindner

Affiliation

¹ Institute of Medical Genetics, Charité, Humboldt University Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.

PMID: 16014370
DOI: 10.1093/bioinformatics/bti571

Abstract

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.

Availability: http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.htm

Contact: [email protected]

Supplementary information: Supplementary information is available on the website. The current version is v4.01beta.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Chromosome Mapping / methods*
Databases, Nucleic Acid
Linkage Disequilibrium / genetics*
Polymorphism, Single Nucleotide / genetics*
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Software*
User-Computer Interface*