search

heche-psb / wgd

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication
https://wgdv2.readthedocs.io/en/latest/
GNU General Public License v3.0
21 stars 0 forks source link

Questions about input file sequence #25

Closed Tang-pro closed 3 months ago

Tang-pro commented 3 months ago

Hi, @heche-psb

When using WGD analysis, can I use the protein sequence directly? Because the full-length transcriptome I constructed currently does not have a cds sequence. Is there any solution?

heche-psb commented 3 months ago

Hi, thanks for your interest in using wgd v2. So far all the analysis in wgd v2 are based on nucleotide sequence (cds). For wgd ksd, it's because we used the codon-level nucleotide alignment for gene tree inference and of course becuase it's needed for the calculation of dS and dN. But for wgd dmd, it's indeed possible to just use protein sequence. I will update functions to accept protein sequences later. Thanks for your suggestion.

Tang-pro commented 3 months ago

@heche-psb , Thank you for your reply, looking forward to your updates!

heche-psb commented 3 months ago

Hi, I have just updated the --prot option into wgd dmd. Please install the latest version 2.0.28 to try it.

Tang-pro commented 3 months ago

Hi , @heche-psb

That is so quick I will try. Thank you! Best!