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Installing MUSCLE · Making an alignment (MSA) · Creating a tree (N-J or UPGMA) · License: MUSCLE is public domain. MUSCLE papers, how to cite. Papers and citing MUSCLE Popular options and features. Alignment output formats · Adding a sequence to an existing MSA · Profile-profile alignment (aligning two MSAs)
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MUSCLE isn't really designed to support a nucleotide matrix, but you can hack it by pretending that AGCT are amino acids and making a 20x20 matrix out of the original 4x4 matrix. You MUST specify the -seqtype protein option to fool MUSCLE into believing that it is aligning amino acid sequences. For more information, see
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If muscle completes successfully, it will create a file seqs.afa containing the alignment. By default, output is created in "aligned FASTA" format (hence the .afa extension). This is just like regular FASTA except that gaps are added in order to align the sequences. This is a nice format for computers but not very readable for
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