Table 5.
Programs for SNP analyses.
| Program | Application | Link | Reference |
|---|---|---|---|
| GATK | Variant discovery and genotyping | https://www.broadinstitute.org/gatk | [76] |
| PLINK | Genome association analysis toolset | http://pngu.mgh.harvard.edu/~purcell/plink | [77] |
| VEGAS and VEGAS2 | Gene-based test for association via SNP association results | http://gump.qimr.edu.au/VEGAS; https://vegas2.qimrberghofer.edu.au | [78,79] |
| Arlequin | Population allele comparison and AMOVA | http://cmpg.unibe.ch/software/arlequin35 | [69,80] |
| Haploview | Haplotype analysis | https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview | [69,81] |
| R/QTL | Mapping quantitative trait loci | http://www.rqtl.org | [82] |
| Triton | Protein mutant construction and activity prediction | http://www.ncbr.muni.cz/triton | [14,83,84] |
| SIFT | Predict amino acid substitution effects | http://sift.bii.a-star.edu.sg/ | [14,85] |
| Polyphen2 | Predict damaging missense mutation | http://genetics.bwh.harvard.edu/pph2 | [14,86] |