Usage

We support the use of WGDI to complete the work on the icon number.

• Dotplot
• Improved collinearity
• Non-synonymous (Ka) and synonymous (Ks)
• BlockInfo
• Correspondence
• BlockKs
• KsPeaks
• PeaksFit
• KsFigure
• Polyploid classification
• ancestral_karyotype
• ancestral_karyotype_repertoire
• karyotype_mapping
• Karyotype
• Shared_fusions
• Alignment
• Alignmenttrees
• Retain
• P-index
• Circos

Common file

• conf

The conf file contains parameters required for the corresponding operation, which are read when WGDI is performed. Using wgdi -* ? > *.conf to get the configuration file in the current directory and modify it to run. If you don’t know which files are needed, you can view it through wgdi -* ? or wgdi -* help or wgdi -* example. These three commands are equivalent.

In conf file: gff1 , lens1 , genome1_name and gff2, lens2, genome2_name represent the files of species 1 and 2 respectively. We will no longer explain these in this documentation.

• gff

Column	Information	Explanation
1	Chr	Chromosome number
2	Id	Gene name
3	Strat	The starting location of a gene
4	End	The ending location of a gene
5	Direction	Direction of a gene sequence
6	Order	Order of each chromosome, starting from 1
7	Original	Original id and not read

• lens

Column	Information	Explanation
1	Chr	Chromosome number
2	Length	Length of chromosome sequences
3	Number	Number of chromosome genes

• blast

The protein-coding genes from each genome were compared against itself and other genomes using BLASTP (e-value < 10-5, and outfmt = 6) or other similar protein sequence searching software ( MMseqs2 , DIAMOND ).

• ancestor file

Required documents for karyotype evolution analysis

Column	Information	Explanation
1	Chr	Chromosome number
2	Start	Homologous regions of these protochromosomes in this genome
3	End	Homologous regions of these protochromosomes in this genome
4	Color	These protochromosomes with different colors
5	Subgenomes	Subgenomes according to protochromosomes

Tips

• You can use wgdi -conf ? > total.conf generates a total.conf file with all parameters, and when you modify the parameters and run WGDI, WGDI will only read the parameters corresponding to the total.conf file to execute your command.

• When a folder runs WGDI, WGDI automatically generates results for you in the background, and you can exit the folder and go to the next folder to start working.

• WGDI performs the conf file for the current folder, so you can copy the conf file in bulk and make parameter modifications appied to the target folder.