Questions about input file sequence
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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?
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.
@heche-psb , Thank you for your reply, looking forward to your updates!
Hi, I have just updated the --prot
option into wgd dmd
. Please install the latest version 2.0.28
to try it.
Hi , @heche-psb
That is so quick I will try. Thank you!
Best!