How could I calculate identity between two 16S rDNA sequence？

epruesse / SINA

SINA - Reference based multiple sequence alignment

https://sina.readthedocs.io

GNU General Public License v3.0

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How could I calculate identity between two 16S rDNA sequence？ #95

Closed fujch7 closed 3 years ago

fujch7 commented 4 years ago

Hi developer,

Thanks for the amazing tool. How could I calculate identity between two 16S rDNA sequence using sina？Just like Pablo Yarza described in his article https://www.nature.com/articles/nrmicro3330

Many thanks

epruesse commented 3 years ago

Hi @fujch7 - while I don't know how Pablo did the identity calculations, I know he was working with ARB. He probably used the distance matrix methods within it. Perhaps it's easiest to contact him directly via his Ribocon email address?

SINA has a number of options how the "fractional identity" can be computed. One of them should get you the same numbers. If not, do open another issue, I might be able to add that.