P-index

The polyploidy index(P-index) is used to characterize the degree of divergence between subgenomes of a polyploidy, to find whether there has been a balanced or unbalanced gene removal from the homoeologous regions.

Parameters

Parameters	Standards and instructions
alignment	Type:file | Default: - Output result of parameter a
gap	type: int | Default: 50 The size of the sliding window.
colors	Type: { color1,color2,color3,– } Default: red,blue,green Set multiple sets of colors based on grouping, split with a comma.
retention	Type: float | Default: 0.05 The region where the retention rate of the sub-genome relative to the reference genome is low, which is 0.05 by default.
diff	Type: float | Default: 0.05 More than this value is considered a significant difference.
remove_delta	Type: bool | Default: true Whether to remove the parameter retention.
savefile	Type:file | Default: - Results of the drawing.

Parameters

Use command to enter the folder wgdi -p ? >> total.conf Take out the parameter file.

[pindex]
alignment = alignment file
gff = gff file
lens =lens file
gap = 50
retention = 0.05
diff = 0.05
remove_delta = (true/false)
savefile = result file

Quick start

After the parameters are modified properly, then run wgdi -p total.conf

Example

The detailed explanation is in the published article