Which one is best software for multiple sequence alignment and primer designing?

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Melline Fontes Noronha

Suggestions..

Primer design - primer3 and PrimerQuest tool

multiple sequence alignment - clustal

Martin Ziegler

Hello Sammuel,

NCBI Primer Blast is a good tool, its a combination of Primer3 and Blast.

Sammuel Shahzad

thanks for suggestions.i am using ugene for MSA then after getting consensus sequence, i am using Primer 3 for primer designing.