Improved collinearity

The algorithm for extracting collinearity is based on the dynamic programming algorithm, similar to the ColinearScan and MCScan.

Parameters

Parameters	Standards and instructions
multiple	Type: int | Default: 1 The best number of homologous genes shown with red dots.
evalue	Type: float | Default: 1e-5 Evalue in the blast result.
score	Type: int | Default: 100 Score value in the blast results.
grading	Type: int , int , int | Default: 50, 40 , 25 Assign different scores based on the colors in the dotplot, with a default of 50 for red, 40 for blue, and 25 for gray.
mg	Type: int , int | Default: 40, 40 The maximum gap(mg) value is an important parameter for detecting collinear regions.
pvalue	Type: float | Default: 1 Evaluate the compactness and uniqueness of collinear blocks, the range is 0-1, and the better collinearity range is 0-0.2.
repeat_number	Type: int | Default: 10 The maximum number of homologous genes is allowed to remove more than part of the population.
process	Type: int | Default: 8 Number of multiple processes.
position	Type: order | Default: order The position of a gene corresponds to the gff file.

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

[collinearity]
gff1 = gff1 file
gff2 = gff2 file
lens1 = lens1 file
lens2 = lens2 file
blast = blast file
blast_reverse = false
multiple  = 1
process = 8
evalue = 1e-5
score = 100
grading = 50,40,25
mg = 40,40
pvalue = 0.2
repeat_number = 10
positon = order
savefile = collinearity file

Quick start

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

Example

The original results are easily accessible at wgdi-example