DISTRUCT protocols

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DISTRUCT specifications

Information


Unique identifier OMICS_12221
Name DISTRUCT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The data to be plotted are specified in ASCII text-formatted files derived from structure output.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Noah A. Rosenberg <>

Publication for DISTRUCT

DISTRUCT in pipelines

 (10)
2017
PMCID: 5376269
PMID: 28392892
DOI: 10.1016/j.csbj.2017.03.002

[…] that there are four genetically distinct sweet cherry subgroups within two larger groups (). in both cases, ‘bing’ segregated into its own group and subgroup. the final graphics files produced by distruct can be seen in , combined with the dendrogram produced by ntsys ()., while wgs enables the largest coverage of the genome, sequencing of random regions reduces the comparable areas across […]

2017
PMCID: 5552028
PMID: 28796789
DOI: 10.1371/journal.pntd.0005718

[…] and correlated allele frequencies. the optimal number of k clusters was chosen using the guidelines from prichard et al. [] and the delta k method [, ]. the results were visualized using the program distruct v.1.1 []., to further explore population structure, discriminant analyses of principle components (dapc), principle component analyses (pca), and plots illustrating fst values were created […]

2017
PMCID: 5737441
PMID: 29045601
DOI: 10.1093/gbe/evx215

[…] populations according to their cluster membership and repeated the above analyses on the reduced data sets as recommended by . results for the identified optimal values of k were visualized using distruct (). we further calculated both locus-specific and population-wide fst () using diversity (), and reconstructed a 2d neighbournet network () based on the pairwise putatively neutral-only […]

2016
PMCID: 4742901
PMID: 26841834
DOI: 10.1038/ncomms10527

[…] used to calculate varying levels of k (k=1–10) and the command choosek.py was used to identify the model complexity that maximized the marginal likelihood (k=8). was generated using the programme distruct. genome-wide ld was estimated using pairwise r2 between snps, which was calculated using the --r2 --ld-window 99999 --ld-window-r2 0 command in plink (version 1.07)., for the gwas diversity […]

2016
PMCID: 4882523
PMID: 27230812
DOI: 10.1038/srep26770

[…] k = 2–4. all analyses were performed with a burn-in length of 20,000, followed by 30,000 mcmc (markov chain monte carlo) replications for each k-value. the solutions for each k were visualized using distruct 1.1., except for the strongest, clearest selective signals, it is difficult to confidently distinguish true signals from false positives using population genetic data alone. thus, […]


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DISTRUCT in publications

 (517)
PMCID: 5919407
PMID: 29698497
DOI: 10.1371/journal.pone.0196276

[…] [], 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 the software distruct software version 1.1 []., to further investigate the genetic structure of each population when adopting an approach without assumptions about hwe or linkage disequilibrium, discriminant […]

PMCID: 5914031
PMID: 29685108
DOI: 10.1186/s12870-018-1284-7

[…] to identify the optimal permuted order of qi matrices with the greatest pairwise similarity. the average of this permutation provided the best qi matrix representation, which was visualized using distruct software []., determinations of the qi threshold at which to infer cluster assignment vary by study, but range from qi = 0.5 [] – 0.8 []. inclusion of wide crosses (f1, f2 and bc1) […]

PMCID: 5898725
PMID: 29652911
DOI: 10.1371/journal.pone.0194842

[…] likely number of clusters, we calculated delta k as proposed by evanno et al. []. the similarity of the runs at each k level was evaluated by the clumpp software as implemented at the online []. the distruct software was used to visualize the best alignment of subpopulation inferring population substructure and individual assignment across the best runs at each k level []., based on a large […]

PMCID: 5891032
PMID: 29630655
DOI: 10.1371/journal.pone.0195591

[…] when qi < 0.80 were considered as admixed genotypes. placement of accessions on the inferred groups was determined using clumpp ver. 1.1 [] and the clumpp output was directly used as input for distruct ver. 1.1 [] to graphically display the results., the degree of differentiation between the genetic groups derived from structure was estimated by performing analyses of molecular variance […]

PMCID: 5882878
PMID: 29615786
DOI: 10.1038/s41598-018-23811-7

[…] among populations. for each k of 1–10 clusters, 10 runs were performed. δk was calculated as previously described. a visual output for the run of highest ln p(d) was generated using the program distruct., several population genetic measurements were used to estimate the extent of genetic diversity in the parasite population according to the nucleotide-length variations in 10 putatively […]


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DISTRUCT institution(s)
Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA

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