how do you align HCoV sequence?

jrotieno / seasonal_HCoV_origins

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how do you align HCoV sequence? #1

Open liamxg opened 5 months ago

liamxg commented 5 months ago

Dear @jrotieno, Could I know how do you align HCoV sequence?

jrotieno commented 4 months ago

Sorry this took a while.

I typically use mafft then inspect the alignment for regions that are not properly aligned. Also depends a lot on the sequences, e.g. are you aligning SARS-CoV-2 sequences only, or like 229E and NL63?

liamxg commented 4 months ago

Dear @jrotieno, Thanks.

I am aligning MERS-CoV.