BarleyGVDB - Barley Genomic Variation Database

PCA / Tree / Population Structure

Choose an analysis type: PCA (scatter + table), Tree (phylogenetic tree), or Structure (population structure bar plot + CV).

Analysis Type:

Genotypic Data: Paste VCF text or upload a VCF file (choose one). The uploaded file must be in VCF format.

VCF (paste text) OR upload file:

Choose File No file chosen

Group Info: Recommended two columns with header: id and Subpopulation (or type).

Group Info (tab/csv) (paste text) OR upload file:

Choose File No file chosen

Sample missingness filter (PLINK --mind)

Site missingness filter (VCFtools --max-missing) (optional)

Number of PCs to calculate

Plot 1 Axes:

X axis

Y axis

Plot 2 Axes:

X axis

Y axis

Figure width (inch)

Figure height (inch)

Show tip labels

Tip label size

Max K

Show sample labels

Sample label size

Group label position

Group label size

Line position

Line size