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Structure Harvester specifications

Information


Unique identifier OMICS_15309
Name Structure Harvester
Interface Web user interface
Restrictions to use None
Input data The STRUCTURE results.
Input format ZIP
Output data A plot of the mean likelihood values per K, a tab-delimited table of the Evanno results.
Programming languages Python
Computer skills Basic
Version 0.9.94
Stability Stable
Source code URL http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/
Maintained Yes

Maintainer


  • person_outline Dent Earl

Information


Unique identifier OMICS_15309
Name Structure Harvester
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The STRUCTURE results.
Input format ZIP
Output data A plot of the mean likelihood values per K, a tab-delimited table of the Evanno results.
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Version 0.9.94
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Dent Earl

Publication for Structure Harvester

Structure Harvester citations

 (908)
library_books

Genetic diversity and structure of tea plant in Qinba area in China by three types of molecular markers

2018
Hereditas
PMCID: 5944026
PMID: 29773972
DOI: 10.1186/s41065-018-0058-4

[…] mate of the most probable number of population. Delta K was plotted against K values; the best number of clusters was determined following the method proposed by Evanno et al. [] and obtained via the Structure Harvester platform (http://taylor0.biology.ucla.edu/structureHarvester/). Delta K reached a maximum value at K = 2, suggesting that the 50 tea germplasm were best divided into two subgroups […]

library_books

Widespread plant specialization in the polyphagous planthopper Hyalesthes obsoletus (Cixiidae), a major vector of stolbur phytoplasma: Evidence of cryptic speciation

2018
PLoS One
PMCID: 5940214
PMID: 29738577
DOI: 10.1371/journal.pone.0196969

[…] was repeated 20 times for each K with 50,000 burn-ins followed by 200,000 MCMC (Markov chain Monte Carlo) iterations using the admixture model and correlated allele frequencies. The web-based program Structure harvester [] was used for visualizing the likelihood plateau of the distribution of LnP(D) and for inferring the most likely number of genetic clusters (ΔK) according to Evanno et al. []. Ad […]

library_books

Deciphering the sexual diploid members of the Boechera suffrutescens complex (Brassicaceae, Boechereae)

2018
PMCID: 5943444
PMID: 29750070
DOI: 10.3897/phytokeys.98.24296

[…] burn-in and 1,000,000 post-burn in generations with 10 iterations for each value of K from 1–11. The most likely value of K for each analysis was identified using the ∆K method of as implemented in STRUCTURE Harvester (). Null alleles at seven loci (B11, C8, BF15, Brdu266, e9, BF3 and BF19), clearly corresponding to either prior taxonomic assignment and/or geographic structure, were coded in STR […]

call_split

Diversity and population structure of red rice germplasm in Bangladesh

2018
PLoS One
PMCID: 5931645
PMID: 29718936
DOI: 10.1371/journal.pone.0196096
call_split See protocol

[…] owing admixture and correlated allele frequency with a 5,000 burn period and a run length of 50,000 were used for conducting model-based structure analysis. Output of analysis was collected using the STRUCTURE harvester [] and identified 4 as the best K value based on the LnP(D) and Evanno’s ΔK []. Principal components analysis (PCA) analysis was conducted also using the STRUCTURE software. In ord […]

library_books

Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic

2018
BMC Evol Biol
PMCID: 5930823
PMID: 29720079
DOI: 10.1186/s12862-018-1179-0

[…] erations per K (after a “burnin” period of 10,000), which ensured stationarity and convergence. The number of groups best-explaining the data was assessed by two commonly used statistics, computed by STRUCTURE HARVESTER []: the average log-likelihood Pr(X│K) [] and the ΔK []. Replicate runs were combined with CLUMPP [] and graphs of assignment probabilities were compiled using DISTRUCT []. We also […]

call_split

Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds

2018
PLoS One
PMCID: 5919407
PMID: 29698497
DOI: 10.1371/journal.pone.0196276
call_split See protocol

[…] bstructures, the most interesting cluster identified with STRUCTURE was re-analysed using the same settings and assuming K = 2 to K = n+3 (n being the number of populations included in each cluster). STRUCTURE HARVESTER [], a web-based program, was used for collating the results generated by the program STRUCTURE. The clustering pattern was implemented in the CLUMPP program and visualised using th […]

Citations

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Structure Harvester institution(s)
Center for Biomolecular Science and Engineering, Biomolecular Engineering Department, University of California, Santa Cruz, CA, USA; Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
Structure Harvester funding source(s)
This work was supported by the National Cancer Institute grants 1U24CA143858-01 and 5R21CA135937.

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