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POPGENE specifications

Information


Unique identifier OMICS_29758
Name POPGENE
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Version 1.32
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Francis Yeh

Additional information


https://sites.ualberta.ca/~fyeh/popgene_info.html

POPGENE citations

 (441)
library_books

Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana

2018
Hereditas
PMCID: 5952850
PMID: 29785177
DOI: 10.1186/s41065-018-0060-x

[…] DNA Analyzer (BiOptic, Taiwan, China) []. The observed numbers of alleles (Na), effective numbers of alleles (Ne), expected heterozygosities (He) and observed heterozygosities (Ho) were determined by Popgene1.32 []. Polymorphism information contents (PIC) were estimated by PowerMarker V3.25 [] (Liu and Muse, 2005). Phylogenetic trees were constructed by PowerMarker V3.25 using the UPGMA method bas […]

call_split

Genetic characterization of indigenous goat breeds in Romania and Hungary with a special focus on genetic resistance to mastitis and gastrointestinal parasitism based on 40 SNPs

2018
PLoS One
PMCID: 5942826
PMID: 29742137
DOI: 10.1371/journal.pone.0197051
call_split See protocol

[…] ewer software (version 1.99, Hoddesdon, UK). The raw allele calls received from LGC Genomics were analyzed with KlusterCaller software from LGC Genomics. Linkage analysis was performed by GENEPOP []. POPGENE 1.32 [] was used to calculate the deviation from Hardy-Weinberg equilibrium (HWE), observed (Ho) and expected (He) heterozygosity values for each studied breed, Polymorphic Information Content […]

library_books

A comprehensive comparison of four species of Onchidiidae provides insights on the morphological and molecular adaptations of invertebrates from shallow seas to wetlands

2018
PLoS One
PMCID: 5919635
PMID: 29698429
DOI: 10.1371/journal.pone.0196252

[…] Ltd., USA). The number of alleles (Na), the observed heterozygosity (HO), the expected heterozygosity (HE) and the deviations from Hardy-Weinberg equilibrium (HWE) for each locus were calculated with Popgene32 (Version 1.32). Bonferroni correction was used to correct the results. The polymorphism information content was calculated with Cervus 3.0 (http://www.fieldgenetics.com/pages/home.jsp). […]

call_split

Genetic diversity in the endangered terrestrial orchid Cypripedium japonicum in East Asia: Insights into population history and implications for conservation

2018
Sci Rep
PMCID: 5915404
PMID: 29691494
DOI: 10.1038/s41598-018-24912-z
call_split See protocol

[…] and clear DNA bands obtained from each ISSR and SCoT primers were scored as absent (0) or present (1). Bands length between 200–1,200 bp (ISSR) and 400–1,500 bp (SCoT) were scored. Using the program Popgene 1.32, and assuming that populations were in Hardy–Weinberg equilibrium, we estimated the following genetic diversity parameters: percentage of polymorphic bands (PPB), observed number of allel […]

library_books

AFLP based genetic diversity of wild orchardgrass germplasm collections from Central Asia and Western China, and the relation to environmental factors

2018
PLoS One
PMCID: 5894997
PMID: 29641553
DOI: 10.1371/journal.pone.0195273

[…] ds (NPB), the percentage of polymorphic bands (PPB) and the polymorphism information content (PIC) [] were calculated by using Excel 2013 software. Shannon information index (Ho) was calculated using POPGENE v3.0 [], assuming populations under Hardy-Weinberg equilibrium (HWE). At species level, NPB, PPB and Ho were calculated. POPGENE v3.0 [] was used to compute the observed number of alleles per […]

call_split

Morphological and Genetic Analysis of Four Color Morphs of Bean Leaf Beetle

2018
PMCID: 5890489
PMID: 29718501
DOI: 10.1093/jisesa/iey016
call_split See protocol

[…] similarity was estimated using the Jaccard index through the SIMQUAL procedure using NTSYSpc (). Dendrograms were constructed to illustrate genetic similarity, following the methodology described by .POPGENE version 1.32 () was used to determine the degree of genetic polymorphisms both within and between color morphs of BLB. Genetic differentiation between color morphs samples was assessed in POPG […]

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