BlockInfo

The color distinction in the dot plot, the collinearity result and the Ks result are integrated into one file. This file contains the main information to achieve the purpose of easily screening the collinearity fragments.

Parameters

Parameters	Standards and instructions
collinearity	Type: file | Default: - Colinearscan or MCScanX result file or gene pairs divided by tab.
score	Type: int | Default: 100 Score value in the blast results.
evalue	Type: float | Default: 1e-5 Evalue value in blast result.
repeat_number	Type: int | Default: 10 The maximum number of homologous genes is allowed to remove more than part of the population.
position	Type: {order} | Default: order The position of a gene corresponds to the gff file.
ks	Type: file | Default: - Ks calculation results.
ks_col	Type: str Default: NG86 The result calculated by ks_YN00 or other methods is a single column.
savefile	Type: file | Default: * .csv Result file.

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

[blockinfo]
blast = blast file
gff1 =  gff1 file
gff2 =  gff2 file
lens1 = lens1 file
lens2 = lens2 file
collinearity = collinearity file
score = 100
evalue = 1e-5
repeat_number = 10
position = order
ks = ks file
ks_col = ks_NG86
savefile = block information (*.csv)

Quick start

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

Example

The original results are easily accessible at wgdi-example

columns	Information
id	Type: str Unique id.
chr1,chr2	Type: int Two chromosomes corresponding to collinearity block.
start1,end1	Type: int The region of chromosome 1 on collinearity block.
start2,end2	Type: int The region of chromosome 2 on collinearity block.
pvalue	Type: float Evaluate the compactness and uniqueness of collinear blocks, the range is 0-1, the better collinearity range is 0-0.2.
length	Type: int The length of collinearity block.
ks_median	Type: float The median of ks value on collinearity block.
ks_average	Type: float The average of ks value on collinearity block.
homo1-5	Type: float The average of scores of different color dots (red=1, blue=0, gray=-1) on synteny blocks.
block1,block2	Type: str Gene pairs in collinear blocks
ks	Type: str Output result of parameter ks.
tandem_ratio	Type: float The density of tandem repeats, in general, a synteny block greater than 0.5 is unreliable.
density1,density2	Type: float Density of collinear blocks.
class1,class2	Type: str Class of collinear blocks.