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PowerMarker specifications


Unique identifier OMICS_20490
Name PowerMarker
Interface Web user interface
Restrictions to use None
Programming languages C#, C++
Computer skills Basic
Stability No
Maintained Yes


  • person_outline Spencer Muse

Publication for PowerMarker

PowerMarker citations


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

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

[…] (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 based on Nei’s (1979) genetic distances []. […]


Diversity and population structure of red rice germplasm in Bangladesh

PLoS One
PMCID: 5931645
PMID: 29718936
DOI: 10.1371/journal.pone.0196096
call_split See protocol

[…] The band-size for each of the markers was scored using the AlphaEaseFC 4.0 software. Using PowerMarker version 3.25 [], summary statistics included the following: the number of alleles, the major allele size and its frequency, gene diversity, and the polymorphism information content (PIC) v […]


Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction Associated DNA Sequencing

PMCID: 5924560
PMID: 29673217
DOI: 10.3390/genes9040218

[…] of GeneAlEx version 6.5 [] was used for further analysis of genetic structure. The genetic distances (GDs) as described by Nei et al. [] between the individuals and populations were calculated using PowerMarker version 3.51 [] and GeneAlex version 6.5 [], respectively. Based on the resulting genetic distance matrix, a neighbor-joining (NJ) phylogenetic tree was constructed using MEGA version 6.0 […]


Association Mapping for Important Agronomic Traits in Safflower (Carthamus tinctorius L.) Core Collection Using Microsatellite Markers

Front Plant Sci
PMCID: 5885069
PMID: 29651296
DOI: 10.3389/fpls.2018.00402

[…] equency (MAF), observed heterozygosity (Ho), expected heterozygosity (He) and degree of polymorphism generated by each marker (computed as polymorphism information content; PIC) were calculated using PowerMarker version 3.25 (Liu and Muse, ). Rare/private allelic richness per locus (Rp) was determined based on rarefaction approach using HP-Rare v.1.0 (Kalinowski, ). Rarefaction allows evaluation o […]


Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry (Physalis peruviana L.)

Front Plant Sci
PMCID: 5869928
PMID: 29616069
DOI: 10.3389/fpls.2018.00362

[…] Standard measures of diversity including Expected Heterozygosity (HE), Observed Heterozygosity (HO), and Polymorphic Information Content (PIC) were calculated by PowerMarker v3.2 (Liu and Muse, ) using filtered SNP markers. The alignment was realized with Bowtie2 (Langmead and Salzberg, ) against the two cape gooseberry references transcriptomes (leaf and root […]


Towards Defining Heterotic Gene Pools in Pearl Millet [Pennisetum glaucum (L.) R. Br.]

Front Plant Sci
PMCID: 5841052
PMID: 29552020
DOI: 10.3389/fpls.2017.01934

[…] ct sizes were scored in base pairs (bp). Further analysis was done using Allelobin 2.0 program (Prasanth et al., ) based on repeat of SSR marker motif to get perfect allele calls.The software package PowerMarker version 3.25 (Liu and Muse, ) was used to determine allele frequency, availability of data, allele number, gene diversity, heterozygosity, and polymorphic information content (PIC) from th […]


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PowerMarker institution(s)
Bioinformatics Research Center, Campus Box 7566, North Carolina State University, Raleigh, NC, USA
PowerMarker funding source(s)
Partly supported by NSF grants DBI-0096033 and DEB-9996118.

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