Re: [Biopython] Struggling with MSA...

Peter Cock <[email protected]> Thu, 15 Feb 2024 16:13:46 +0000
Newsgroups gmane.comp.python.bio.general
Message-ID <CAKVJ-_6Q_8CEbufb=EbWWexQrCEh4Kgu86XJBMhNGmqOornEhw@mail.gmail.com>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=