Introduction

The WGDI workflow consists of three main parts: (1) Polyploidy inference using Dotplot, Collinearity extraction, Ks distributions (2) Hierarchical inference of genomic homology resulted from recursive paleopolyploidizations. (3) Subgenomic and ancestral genome reconstruction and other evolutionary scenarios.

WGDI contains multiple subroutines, the user only needs to modify the configuration file simply, and then enter the name of the subroutine to be executed, Such as wgdi -d your.conf. In the following, we will describe in detail the subroutines of WGDI software.

WGDI subroutine and function

Parameters		Functions
-h	Help	Show help message and exit
-v	Version	Show program’s version number
-d	DotPlot	Show homologous gene dotplot
-icl	Collinearity	Improved version of ColinearScan
-ks	CalKs	Calculate Ka/Ks for homologous gene pairs by YN00
-bi	BlockInfo	Collinearity and Ks speculate whole genome duplication
-c	Correspondence	Extract event-related genomic alignment
-bk	BlockKs	Show Ks of blocks in a dotplot
-kp	KsPeaks	A simple way to get ks peaks
-pf	PeaksFit	Gaussian fitting of ks distribution
-pc	polyploidy_classification	Show event-related genomic alignment in a dotplot
-km	karotype_mapping	Mapping from the known karyotype result to this species
-k	karotype	Show genome evolution from reconstructed ancestors
-a	Alignment	Alignment of hierarchical and event-related gene collinearity
-at	AlignmentTrees	Phylogenetic trees constructed by collinear genes
-p	P-index	Polyploidy-index characterize the degree of divergence among subgenomes of a polyploidy
-r	Retain	Show subgenomes in gene retention or genome fractionation
-ci	Circos	A simple way to run circos
-conf	Configure	Display and modify the environment variable