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AIS specifications


Unique identifier OMICS_29892
Name AIS
Alternative name Alleles in Space
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A file with sets of spatial coordinates for each observation in the dataset and a file including genetic data for each individual.
Operating system Windows
Computer skills Advanced
Stability Stable
Registration required Yes
Maintained Yes


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  • person_outline Mark Miller <>
  • person_outline Mark Miller <>

Publication for Alleles in Space

AIS in publications

PMCID: 4355488
PMID: 25756994
DOI: 10.1371/journal.pone.0120645

[…] by pritchard et al. [] and the δk statistic according to evanno et al. []. the occurrence of barriers between populations was tested using monmonier´s maximum difference algorithm implemented by alleles in space []., the number of populations, and the occurrence of genetic discontinuities among them, were also inferred by a spatial explicit bayesian model based on simulations […]

PMCID: 3960240
PMID: 24647580
DOI: 10.1371/journal.pone.0092274

[…] quantified deviations from hardy-weinberg equilibrium (hwe) by estimating f is in genepop with 10,000 iterations., we evaluated rangewide isolation by distance by using a mantel test performed in alleles in space (ais, version 1.0; ) to determine whether a significant correlation existed between pairwise matrices of nei's genetic distances and geographic distances matrices. […]

PMCID: 3953067
PMID: 24625572
DOI: 10.1371/journal.pntd.0002734

[…] was selected according to the highest significant (p<0.001) value., an interpolation-based graphical method was employed to generate a three-dimensional genetic landscape shape (gls) within the alleles in space (ais) program . this analysis provides a visual perspective of the spatial distribution of the genetic structure over landscapes, with peaks in areas where pairwise genetic distances […]

PMCID: 3873191
PMID: 24385863
DOI: 10.1590/S1415-47572013000400018

[…] of genetic structure in pumas we assessed the correlation between genetic and geographic distances for all pairs of sampled individuals using a mantel test (). this was performed with the program alleles in space (ais) (), employing the proportion of differences (i.e. a p-distance equivalent) to generate the genetic distance matrix and 10,000 permutations to assess statistical significance. […]

PMCID: 3915079
PMID: 24523566
DOI: 10.1007/s10764-013-9725-5

[…] 0 (no differentiation, high gene flow) to 1 (complete differentiation, no gene flow), were used to evaluate the amount of gene flow within each species at the three respective spatial levels. using alleles in space (ais) 1.0 (miller ) we furthermore quantitatively analyzed the correlation between genetic and geographic distances with a mantel test (mantel ) for each species, testing […]

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AIS institution(s)
Department of Biology, Utah State University, Logan, UT, USA

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