GENETIX protocols

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GENETIX specifications

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Unique identifier OMICS_22207
Name GENETIX
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Version 4.05
Stability Stable
Maintained Yes

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GENETIX in pipelines

 (57)
2018
PMCID: 5817159
PMID: 29468047
DOI: 10.1002/ece3.3821

[…] tree and relatedness plot. the first three axes of variation were used in principal component analysis (pca) plots. additionally, factorial correspondence analysis (fca) plots were generated in genetix 4.05.2 (belkhir, borsa, chikhi, raufaste, & bonhomme, ) from the same snp dataset., pairwise population f st values were estimated among populations inferred from these analyses using […]

2018
PMCID: 5817159
PMID: 29468047
DOI: 10.1002/ece3.3821

[…] combating the dearth of genetic data available for labeobarbus and other cyprinids., raw sequence data, processed input files for the final dataset (structure, genepop, fineradstructure, arlequin, genetix, diyabc, geste/bayescan, and vcf), and regular expressions for removing adapter pollution are available from the dryad digital repository: https://doi.org/10.5061/dryad.g00b7., p.b. […]

2018
PMCID: 5819644
PMID: 29463303
DOI: 10.1186/s13104-018-3249-1

[…] for multiple testing, the p value threshold was adjusted with bonferroni correction. number of alleles na, observed heterozygosity ho and expected heterozygosity he were calculated with the software genetix v4.05 [, see table 2]. the same procedures were also performed on samples from the willow grouse, which were collected from two different areas 124 km apart in norway and in sweden (table )., […]

2018
PMCID: 5859023
PMID: 29555926
DOI: 10.1038/s41598-018-23004-2

[…] observed (ho) and expected (he) heterozygosities were estimated using arlequin v. 3.11. deviations from hardy-weinberg equilibrium (hwe) were characterized by the inbreeding coefficient (fis) with genetix v. 4.05 and p-values where calculated genepop v. 4.2. putative scoring errors were checked with micro-checker v. 2.2.3 and freena v. 9.3 was used to to evaluate possible differences […]

2017
PMCID: 5301200
PMID: 28186200
DOI: 10.1038/srep42416

[…] trend test implemented in past. pairwise differences in allelic frequencies between decades were estimated for each river using genepop. fst values of genetic differentiation were estimated using genetix v.4.04 and significances were determined with 1000 permutations to correct for simultaneous tests, strict bonferroni corrections were applied., structure v2.3.3 was used to test how many […]


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GENETIX in publications

 (852)
PMCID: 5942175
PMID: 29765202
DOI: 10.2147/DDDT.S156826

[…] to cell cycle analysis using guava easycyte 8ht benchtop flow cytometer (merck & co., inc., whitehouse station, nj, usa)., approximately 1×105 pc-3 cells/ml were plated in a 96-well plate (genetix usa inc, san jose, ca, usa) and incubated for 24 h at 37°c with 5% co2. the pc-3 cells were then exposed to 6 μg/ml koenimbin for 48 h. a cellomics multiparameter cytotoxicity 3 kit […]

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

[…] version 4.0 software []. level of significance were adjusted using false discovery rate (fdr) procedure []., the fis for each population was calculated via bootstrapping using 1,000 replicates with genetix software version 4.05 []. the extent of population subdivision was investigated by calculating the global multi-locus fst value. the index of pairwise fst of weir and cockerham [] […]

PMCID: 5919678
PMID: 29698484
DOI: 10.1371/journal.pone.0196409

[…] as template were optimized. the optimised qpcr assay consisted of 2μl (100-10fg) of template dna, 1μl of the forward and reverse primers each (1μm), 10μl of pcr master mix with sybr green buffer (genetix, india) in a reaction volume of 20μl. the volume was adjusted with nuclease free water. all experiments were performed in triplicate., light cycler conditions were as follows: 95°c for 5 min, […]

PMCID: 5927189
PMID: 29731643
DOI: 10.2147/IDR.S156593

[…] polymerase chain reaction (pcr) at kathmandu center for genomics and research laboratory (kcgrl)., the bacterial plasmid dna was extracted using surespin plasmid mini kit catalogue no.np-37105 (genetix biotech, new delhi, india) following the manufacturer’s instructions. briefly, a single colony from each phenotypic esbl-producing isolate was transferred to luria–bertani broth and incubated […]

PMCID: 5919042
PMID: 29694435
DOI: 10.1371/journal.pone.0196124

[…] if the mlgs were separated by less than two stepwise mutations, they were grouped together into a single multilocus lineage (mll). the second method consisted of a factorial discriminant analysis in genetix [], which is a multivariate analysis approach that uses no a priori genetic assumptions for relationships between allelic differences and genetic distance., to detect the signature of asexual […]


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