IBDWS protocols

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IBDWS specifications

Information


Unique identifier OMICS_16713
Name IBDWS
Alternative name Isolation by Distance Web Service
Interface Web user interface
Restrictions to use None
Input data Some genetic data with or without corresponding geographical information.
Input format TXT,HTML
License GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Jeffrey Jensen <>
  • person_outline Andrew Bonohak <>
  • person_outline Scott Kelley <>

Information


Unique identifier OMICS_16713
Name IBDWS
Alternative name Isolation by Distance Web Service
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data Some genetic data with or without corresponding geographical information.
Input format TXT,HTML
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Medium
Version 2.1
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Jeffrey Jensen <>
  • person_outline Andrew Bonohak <>
  • person_outline Scott Kelley <>

Publication for Isolation by Distance Web Service

IBDWS in pipelines

 (15)
2016
PMCID: 4801968
PMID: 27087930
DOI: 10.1002/ece3.1957

[…] the minimum population sample size (n = 5). isolation‐by‐distance scenarios were tested using mantel tests to correlate f st and log‐transformed geographic distances as implemented in the software ibdws version 3.23 (bohonak )., the nested sampling regime (several populations per island, with several islands under consideration) allowed to discern between within‐ and between‐island […]

2016
PMCID: 4842280
PMID: 27108406
DOI: 10.1186/s13071-016-1513-6

[…] genetics distances were used to construct unrooted upgma tree in phylip 3.695 [] to infer population clustering. isolation-by-distance among populations was explored with mantel tests [] using the isolation by distance web service v3.23 []. euclidian geographical distances among the 15 populations were calculated based on geographical coordinates using great circle calculations to accurately […]

2016
PMCID: 4876407
PMID: 27210568
DOI: 10.1038/srep26613

[…] version 2.2. to verify the association between genetic isolation and geographical distance, mantel tests with 10,000 randomisations were performed on both nrits and cpdna using the web service of ibdws version 3.23 (http://ibdws.sdsu.edu/~ibdws/distances.html)., according to the results from samova, barrier and monsoonal climatic characteristics of their geological locations, all populations […]

2016
PMCID: 5056711
PMID: 27723778
DOI: 10.1371/journal.pone.0164441

[…] of molecular variance (samova) using the ssr and mtdna (all concatenated data) datasets separately in samova 2.0 []. for further information, see ., we also implemented the mantel test using the isolation by distance web service 3.23 (ibdws) [] to investigate the potential correlation between genetic (pairwise φst) and geographic (in kilometres) distances, considering all populations. […]

2015
PMCID: 4420266
PMID: 25942425
DOI: 10.1371/journal.pone.0126309

[…] infer the affinity between bats from summering sites and swarming sites. as well, we conducted an ibd analysis between microsatellite and geographic distance data using a mantel test implemented in ibdws on summering and swarming sites separately., if females are philopatric to summering sites, a greater level of relatedness should occur between individuals at these sites relative […]


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IBDWS in publications

 (138)
PMCID: 5883011
PMID: 29615795
DOI: 10.1038/s41598-018-23986-z

[…] estimations were obtained from the 300,000 iterations that followed a burn-in period of 100,000 iterations. the correlation between genetic distance and geographic distance was assessed using ibdws version 3.21. additionally, the distribution of genetic variation was analyzed by amova analysis using the arlequin suite version 3.5. principal components analysis (pca) was performed using […]

PMCID: 5938445
PMID: 29760881
DOI: 10.1002/ece3.3993

[…] from 10,000 permutations in arlequin 3.5.1.2 (excoffier et al., ). finally, isolation‐by‐distance (ibd) analysis was performed using a pairwise f st matrix, with a mantel test between populations in ibdws (http://ibdws.sdsu.edu/~ibdws; bohonak, ; jensen, bohonak, & kelley, ), to test for correlation between genetic and geographic distances., in total, 765 base pairs (bp) of the mtdna control […]

PMCID: 5868808
PMID: 29579060
DOI: 10.1371/journal.pone.0194646

[…] distances (km) between sampled populations were estimated using google earth 4.3 and plotted against pairwise genetic distance []. ibd regressions were performed online using the ibd web service (ibdws, http://phage.sdsu.edu/~jensen/) [] with 10,000 data randomizations. the extent of population differentiation among samples using microsatellites was visualized with discriminant analysis […]

PMCID: 5838013
PMID: 29545814
DOI: 10.3389/fpls.2018.00246

[…] we tested for a correlation between pairwise population genetic distance (rst) and geographic distance among sampling locations (isolation-by-distance effect) using a mantel test (mantel, ) in ibdws (isolation by distance web service) v3.21 (jensen et al., ) with 10,000 permutations to determine the significance of ibd pattern. additionally, we calculated the pollen/seed migration ratio […]

PMCID: 5821360
PMID: 29466431
DOI: 10.1371/journal.pone.0193220

[…] genotypes and mtdna cr sequences, respectively. we tested for correlations between matrices of genetic distance (fst or φst) and geographic distance using a mantel test as implemented in the package ibdws v. 3.2.3 (http://ibdws.sdsu.edu/~ibdws/) [], with 1000 random permutations to test for significance., the isolation-with-migration model (im) [] was used to examine the relative contribution […]


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IBDWS institution(s)
High Tech High, San Diego, CA, USA; Department of Biology, San Diego State University, San Diego, CA, USA

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