The number of gene pairs in the KS result file is not equal to the number of gene pairs in collinearity file

SunPengChuan / wgdi

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

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The number of gene pairs in the KS result file is not equal to the number of gene pairs in collinearity file #49

Closed cfz1998 closed 5 months ago

cfz1998 commented 5 months ago

Hi.@SunPengChuan

My collinear file has 40,528 gene pairs. Why does the result Ks file have only 23,960 gene pairs?

[ks]
cds_file = all.cds.fa
#cat all cds files together
pep_file = all.pep.fa
#cat all pep files together
align_software = mafft
pairs_file = A_A.collinear
ks_file = A_A.ks

A_A.collinear: 40,528 gene pairs A_A.ks: 23,960 gene pairs

SunPengChuan commented 5 months ago

Two genes (gene1 vs gene2) of the same species are equivalent to (gene2 vs gene1), thus eliminating numerous distinct combinations.

cfz1998 commented 5 months ago

Thank you for your reply!