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GENIE specifications

Information


Unique identifier OMICS_13090
Name GENIE
Alternative name GENealogy Interval Explorer
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data Estimated phylogenies
Output data Demographic models and skyline plot, and a log file
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Oliver Phybus

Publication for GENealogy Interval Explorer

GENIE citations

 (6)
call_split

Biased phylodynamic inferences from analysing clusters of viral sequences

2017
Virus Evol
PMCID: 5570026
PMID: 28852573
DOI: 10.1093/ve/vex020
call_split See protocol

[…] Coalescent phylogenies were simulated in GENIE v3.0 (), with the population size in the present, N(0) equal to 1,000 generations, and the exponential growth rate, r, equal to 0.5. Trees with 200, 400, 600, and 800 tips were simulated under e […]

library_books

Lifestyle and Ice: The Relationship between Ecological Specialization and Response to Pleistocene Climate Change

2015
PLoS One
PMCID: 4636791
PMID: 26535569
DOI: 10.1371/journal.pone.0138766

[…] ability of datasets is sufficient for reconstruction of more than one coalescence interval. We generated ultrametric genealogies for each species in PAUP* 4.0 [] under the strict clock model and used Genie v3.0 [] for skyline plot reconstruction. The optimal value of the parameter ε, which controls the grouping of adjacent coalescence intervals, was chosen by maximizing the log LAICc function of t […]

call_split

Dated Phylogenies of the Sister Genera Macaranga and Mallotus (Euphorbiaceae): Congruence in Historical Biogeographic Patterns?

2014
PLoS One
PMCID: 3894986
PMID: 24465660
DOI: 10.1371/journal.pone.0085713
call_split See protocol

[…] l analyses.We visually assessed the temporal accumulation of lineages in Macaranga and Mallotus by plotting lineages-through-time (LTT) based on the excised ingroups from our BEAST MCMC chronogram in GENIE v3.0 . To evaluate the effects of incomplete taxon sampling on the slope of our empirical LTT curves, we generated 1000 simulated trees based on the extant number of recognized species in each g […]

call_split

Diversification of myco heterotrophic angiosperms: Evidence from Burmanniaceae

2008
BMC Evol Biol
PMCID: 2492876
PMID: 18573195
DOI: 10.1186/1471-2148-8-178
call_split See protocol

[…] mber of lineages that must be missing to obtain a γ-statistic as extreme as the measured one if γ actually is zero []. The resulting curves are shown in Figure . All γ-statistics were calculated with Genie 3.0 []. […]

library_books

Sex and virulence in Escherichia coli: an evolutionary perspective

2006
Mol Microbiol
PMCID: 1557465
PMID: 16689791
DOI: 10.1111/j.1365-2958.2006.05172.x

[…] uated with a generalized skyline plot based on the distribution of coalescence events within a phylogenetic tree using the Tamura-Nei model of evolution (gamma = 0.312; invariable sites = 0.642) with GENIE (). GENIE was also used to calculate the likelihoods according to the coalescent probability distribution on the basis of different demographic models such as exponential or logistic growth. The […]

call_split

Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal

2005
BMC Evol Biol
PMCID: 1325260
PMID: 16332256
DOI: 10.1186/1471-2148-5-70
call_split See protocol

[…] d with SeqGen [] using the phylogenetic trees and model parameters previously obtained. A lineages through time plot of an ultrametric tree obtained with these methods was calculated with the program GENIE []. […]

Citations

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GENIE institution(s)
Department of Zoology, University of Oxford, Oxford, UK
GENIE funding source(s)
The Wellcome Trust (grant 50275) and The Royal Society

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