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phylogeo specifications


Unique identifier OMICS_08471
Name phylogeo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Zachary Charlop-Powers <>

Publication for phylogeo

phylogeo citations


Development of microsatellite markers for the wind cave–associated shrub Lonicera alpigena subsp. glehnii (Caprifoliaceae)

PMCID: 5828129
PMID: 29732245
DOI: 10.1002/aps3.1014

[…] pcr amplification., voucher and locality information are provided in appendix ., we developed 18 polymorphic simple sequence repeat markers in l. alpigena subsp. glehnii, which will be valuable for phylogeo‐graphic studies and conservation genetics of this wind cave–associated taxon, as well as for population genetics of other lonicera species., this work was supported by the japan society […]


Origin, evolution, and global transmission of community acquired Staphylococcus aureus ST8

PMCID: 5724248
PMID: 29158405
DOI: 10.1073/pnas.1702472114

[…] with treeannotator v.1.8.2 and used for graphical representation of the data. a .kml file to visualize the phylogeographic spread using google earth was created from the mcc tree using the phylogeo.jar script developed by trevor bedford (, accessed april 2016) ()., we searched for the presence or absence of genes and unique […]


Historical and contemporary factors generate unique butterfly communities on islands

PMCID: 4926222
PMID: 27353723
DOI: 10.1038/srep28828

[…] framework programme (project no. 625997). l. dapporto was supported by european union’s horizon 2020 research and innovation programme under the marie sklodowska-curie grant (project no. 658844 eco-phylogeo). we thank axel hausmann, anthony seguna and michael seizmair for providing samples and alessandro cini, david baracchi and giuseppe mazza for their help in field collections., author […]


Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

PMCID: 4959494
PMID: 26944846
DOI: 10.1128/AEM.03821-15

[…] were estimated by discrete phylogeographic analysis using a standard continuous-time markov chain (ctmc) () implemented in beast. a location-annotated mcc tree was converted to the kml format using phylogeo.jar, which is relatively equivalent to spread ( the kml file was then visualized in google earth (, the demographic […]


Cryptic animal species are homogeneously distributed among taxa and biogeographical regions

PMCID: 1939701
PMID: 17640383
DOI: 10.1186/1471-2148-7-121

[…] abstract and keywords as well as some articles being not in english. the final search string, finding 771,931 entries, was [phylogen* or taxonom* or systemat* or morpholog* or tax* or discover* or phylogeo* or population genet* or kary* or genetic* struct* or population struct* or population different* or speciat* or identificat* or diversi* or descript* or new spec* or biodiv* or spec* […]

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phylogeo institution(s)
Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
phylogeo funding source(s)
This work was supported by National Institutes of Health grant number GM077516 and AI110029.

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