Table 1 Dimension reduction-based methods of population structure analysis
From: Nonparametric approaches for population structure analysis
Reference | Dimension reduction | Distance matrix | Clustering | Tool/package |
|---|---|---|---|---|
Patterson at el. (2006) [41] | PCA (TW) | – | – | EIGENSTRAT/smartpca [82]: Perl |
Liu at el. (2006) [40] | SVD | Cosine similarity | Density-based mean clustering (DBMC) | – |
Lee at el.(2009) [52] | PCA (TW) | – | Spectral clustering (K-means, mixture model) | – |
Intarapanich at el. (2009) [11] | PCA (TW) | Euclidean distance | Fuzzy C-means | TW-ipPCA [83]: MATLAB |
Limpiti at el.(2011) [16] | PCA (EigenDev) | Euclidean distance | Fuzzy C-means | EigenDev-ipPCA [83]: MATLAB |
Amornbunchornvej at el. (2012) [58] | PCA | ASD | Ward’s clustering | – |