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Associated diseases

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LDx specifications

Information


Unique identifier OMICS_05834
Name LDx
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for LDx

LDx in publications

 (2)
PMCID: 5400383
PMID: 28087779
DOI: 10.1093/molbev/msw282

[…] and selection treatment and age as the two factors (pic ∼ treatment + age). α = 0.05 was bonferroni corrected with the number of snp loci tested (0.05/1,142,812 = 4.37e−08)., we calculated ld using ldx, a method which uses an approximate maximum likelihood approach to estimate ld (r2) from pooled resequencing data (), using hpc resources provided by the texas advanced computing center (tacc) […]

PMCID: 5133387
PMID: 27871090
DOI: 10.1038/nature20151

[…] estimates between strains due to differing coverage, but not affecting diversity comparisons within strains., linkage disequilibrium between the snps was determined for the por and jean strains with ldx, assuming physical linkage between alleles on the same read or read pairs. r2 was determined by a maximum likelihood estimator, minimum and maximum read depths corresponded to the 2.5% and 97.5% […]


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LDx institution(s)
Department of Biology, Stanford University, Stanford, CA, USA

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