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Loki specifications


Unique identifier OMICS_09402
Name Loki
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.4.5
Stability Stable
Maintained Yes




No version available


  • person_outline Elizabeth Thompson

Publication for Loki

Loki citations


Genetic variation and gene expression across multiple tissues and developmental stages in a non human primate

Nat Genet
PMCID: 5714271
PMID: 29083405
DOI: 10.1038/ng.3959
call_split See protocol

[…] pping Set consists of 147,967 SNPs on the 29 vervet autosomes. This set has, on average, 58.2 SNPs per Mb of vervet sequence, with an average gap of 17.5 Kb between adjacent SNPs.The software package Loki, which implements Markov Chain Monte Carlo methods, was used to estimate multipoint identical by decent (MIBD) allele-sharing among all vervet family members from the genotype data. As long stret […]


Heritability and Preliminary Genome Wide Linkage Analysis of Arsenic Metabolites in Urine

Environ Health Perspect
PMCID: 3621197
PMID: 23322787
DOI: 10.1289/ehp.1205305

[…] entity-by-descent (IBD) matrices [for details on model formulation, see Supplemental Material, pp, 2–3 (http://dx.doi.org/10.1289/ehp.1205305)]. We computed multipoint IBD matrices using the software Loki (; ) by using STR marker map positions obtained based on the DeCode map (). At each chromosomal location, SOLAR conducts likelihood ratio tests comparing a model that estimates the unexplained va […]


The endocrine stress response is linked to one specific locus on chromosome 3 in a mouse model based on extremes in trait anxiety

BMC Genomics
PMCID: 3557225
PMID: 23114097
DOI: 10.1186/1471-2164-13-579
call_split See protocol

[…] rimax rotation were performed using the open-source statistical software package R ( http://www.r-project.org/). PC analysis was carried out using the normalised phenotypic data of male mice only.The Loki package [,] for multipoint IBD estimations and oligogenic model for segregation and linkage analysis were used to benefit from the entire three-generation pedigree and to implement reversible ju […]


A gene frequency model for QTL mapping using Bayesian inference

PMCID: 2901203
PMID: 20540762
DOI: 10.1186/1297-9686-42-21

[…] en shown to successfully detect linkage for multiallelic QTLs [-]. A comparison between the performance of mutiallelic and biallelic analyses under multiallelic modes of inheritance using the package Loki and the multiallelic version of Loki (maLoki) was done by Rosenthal et al. [] using both simulated and real data. For simulated data a four-generation pedigree with 98 individuals was simulated t […]


Linkage disequilibrium across two different single nucleotide polymorphism genome scans

BMC Genet
PMCID: 1866694
PMID: 16451701
DOI: 10.1186/1471-2156-6-S1-S86

[…] ). All LD and PIC measures were assigned to the average genetic distance between the markers forming each pair.For AMA and ILP SNP markers on chromosomes 3 and 18, MIBD matrices were calculated using LOKI []. Chromosomes 18 and 3 were selected because they showed candidate regions with LOD scores ≥ 3 for COGA's ttdt3 electrophysiological trait phenotype. These MIBDs were a mixture of individual SN […]


Multipoint identity by descent computations for single point polymorphism and microsatellite maps

BMC Genet
PMCID: 1866751
PMID: 16451644
DOI: 10.1186/1471-2156-6-S1-S34

[…] al with SNP markers, the large size of some of these pedigrees required extensive trimming because the basic algorithm still computes all possible inheritance vectors. We therefore decided to use the LOKI software to generate IBD matrices.LOKI uses Markov chain Monte Carlo (MCMC) methodology to repeatedly sample possible segregation patterns. However, determining appropriate run length (number of […]


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Loki institution(s)
Department of Statistics, University of Washington, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA; Division of Medical Genetics, University of Washington, Seattle, WA, USA

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