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SunPengChuan / wgdi

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
https://wgdi.readthedocs.io/en/latest/
BSD 2-Clause "Simplified" License
114 stars 22 forks source link

Karyotype Evolution #45

Closed amvarani closed 8 months ago

amvarani commented 9 months ago

Dear @SunPengChuan , I need your help again

I was following your documentation on: https://github.com/SunPengChuan/wgdi-example/blob/main/Karyotype_Evolution.md and trying to generate a paleogenomics analysis of my species, which is close to Populus-Salix.

Following the example, I got it image

After using -bk my results are: image

Finally, when I map using the -km to map AEK I got only seven chromossomes from the AEK, and have this:

image

I would also like to plot the Karyotype style figure. Can you help me ?

SunPengChuan commented 9 months ago

The process of chromosomal evolution presented here deviates considerably from prior methodologies, moving beyond a mere straightforward mapping. The emphasis is placed on identifying both the shared and unique chromosomal structural variations across different species, providing a more nuanced understanding of genetic diversity.