Table 7. Summaries of inversion analysis tools.
Details of existing software tools that were either designed or can be applied to inversion analysis using SNP data are summarized.
| SNPRelate | PCAdapt | Asaph | inveRsion | invClust | EIGENSOFT | PLINK | |
|---|---|---|---|---|---|---|---|
| Paper | [34] | [35, 36] | [16] | [56, 62] | [15] | [29, 31] | [63, 64] |
| Language | R | C and R | Python | R | R | C | C |
| Summary | SNPRelate provides parallel implementations of PCA for SNP data and the ability to perform correlation testing between PC coordinates and SNP genotypes. Although not designed for inversion detection, SNPRelate can be applied to inversion detection using PCA scatter and Manhattan plots. | PCAdapt uses PCA to infer population structure and assumes variants with strong associations with the PC coordinates are under local selection. Although not designed for inversion detection, PCA scatter plots and variant p-values from association tests can be used to detect inversions with scatter and Manhattan plots, respectively. | Asaph uses PCA, clustering, and association tests to detect, genotype, and localize inversions. | inveRsion identifies changes in linkage disequilibrium along the chromosome arm from SNP data to find inversion breakpoints. | Developed by the authors of inveRsion, invClust performs PCA and clustering of samples with Gaussian mixture models to perform inversion genotype inference. Inversions can first be detected and localized by inveRsion and then invClust can be applied to SNPs in the inversion region. | EIGENSOFT provides analysis of population structure using PCA. | PLINK can perform population inference with PCA and perform regression with quantitative traits. Although not the intended purpose, these techniques can be used for inversion analysis. |
| Year Released | 2012 | 2014 (C) / 2016 (R) | 2018 | 2012 | 2015 | 2006 | 2007 |
| Inversion Detection | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
| Genotyping | Yes | Yes | Yes | No | Yes | Yes | Yes |
| Localization | Yes | Yes | Yes | Yes | No | No | Yes |
| Software Link | https://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html | https://cran.r-project.org/web/packages/pcadapt/index.html | https://github.com/rnowling/asaph | https://www.bioconductor.org/packages/release/bioc/html/inveRsion.html | https://rdrr.io/github/isglobal-brge/invClust/ | https://github.com/DReichLab/EIG | https://www.cog-genomics.org/plink/1.9/ |