Identify conserved regions in SARS-COV2 virus based on Multiple sequence alignment for primer design
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3 months ago

As a part of my project, i am supposed to download sequences from (GISAID) that are representative of the 3 waves inside Africa and perform multiple sequence alignment, based on which i should find the conserved region to use as a target for primer design. I am wondering if there is a certain tool or script that would do so? and what parameters can i set for choosing the most accurate conserved region in terms of length and position, gaps etc

alignment MSA conserved primer design sequence Multiple region • 287 views
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I gave them a quick read, couldn't find any mention of tools or scripts used to identify and extract conserved region from multiple sequence alignment file

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