HKA protocols

HKA specifications

Information


Unique identifier OMICS_17390
Name HKA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Source code URL https://bio.cst.temple.edu/~hey/downloads/HKA_source.zip
Maintained Yes

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Documentation


Maintainer


  • person_outline Jody Hey <>

Publication for HKA

HKA IN pipelines

 (7)
2016
PMCID: 4964047
PMID: 27468897
DOI: 10.1186/s13059-016-1027-8

[…] between the pantro2 and hg19 reference assemblies and selecting the coincident sets of human and chimpanzee snps., to verify the signatures of tajima’s d, we also performed a hudson–kreitman–aguade (hka) test in the eur panel (additional file 1: figure s2a, b). the hka test compares the level of polymorphism (within-species diversity) to the level of substitution (between-species divergence). […]

2016
PMCID: 4964047
PMID: 27468897
DOI: 10.1186/s13059-016-1027-8

[…] coincident sets of human and chimpanzee snps., to verify the signatures of tajima’s d, we also performed a hudson–kreitman–aguade (hka) test in the eur panel (additional file 1: figure s2a, b). the hka test compares the level of polymorphism (within-species diversity) to the level of substitution (between-species divergence). we conducted the maximum likelihood hka test [16] by using the mlhka […]

2016
PMCID: 4964047
PMID: 27468897
DOI: 10.1186/s13059-016-1027-8

[…] file 1: figure s2a, b). the hka test compares the level of polymorphism (within-species diversity) to the level of substitution (between-species divergence). we conducted the maximum likelihood hka test [16] by using the mlhka software (http://wright.eeb.utoronto.ca/programs/). the surrounding 1-kb regions of the dnase footprint snps were compared with 99 neutrally evolved regions […]

2013
PMCID: 3598968
PMID: 23289814
DOI: 10.1186/1471-2148-13-3

[…] no intragenic recombination or selection we tested each locus for recombination using the pairwise homoplasy index [83] implemented in phipack [84], and for selection performing multiple loci hka tests [85] using sites and hka [86]., to obtain a multilocus perspective of the diversification within the whole clade, we employed the bayesian mcmc method from heled and drummond [87], *beast, […]

2013
PMCID: 3598968
PMID: 23289814
DOI: 10.1186/1471-2148-13-3

[…] or selection we tested each locus for recombination using the pairwise homoplasy index [83] implemented in phipack [84], and for selection performing multiple loci hka tests [85] using sites and hka [86]., to obtain a multilocus perspective of the diversification within the whole clade, we employed the bayesian mcmc method from heled and drummond [87], *beast, implemented in beastv1.6.1 […]

HKA institution(s)
National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA

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