Alignment

Alignment of hierarchical and event-related gene collinearity.

Parameters

Parameters	Standards and instructions
blockinfo	Type: file | Default: - Output result of parameter bi
colors	Type: { color1,color2,color3,– } Default: red,blue,green Set multiple sets of colors based on grouping, split with a comma.
position	Type: {order, start , end } | Default: order The position of the gene corresponds to the gff file.
blockinfo_reverse	Type: bool | Default: false The two species aligned swap positions..
figsize	Type: int,int | Default: 10,10 Control the proportion of the size of the saved picture.
savefile	Type: file | Default: * .csv Result file.
markersize	Type: float | Default: 0.5 The size of the point in the plot.
savefig	Type: {*. png, *. pdf, *. svg} | Default: *. png Save pictures support png, pdf, svg formats.

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

[alignment]
gff1 =  gff1 file
gff2 =  gff2 file
lens1 = lens1 file
lens2 = lens2 file
genome1_name =  Genome1 name
genome2_name =  Genome2 name
markersize = 0.5
position = order
colors = red,blue,green
figsize = 10,10
savefile = savefile(.csv)
savefig= save image
blockinfo = block information file
blockinfo_reverse = false

Quick start

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

Example

The original results are easily accessible at wgdi-example