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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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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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Write output in CLUSTALW format with the "CLUSTAL W (1.81)" header rather than the MUSCLE version. This is useful when a post-processing step is picky about the file header. core. yes in muscle,. no in muscled. Do not catch exceptions. diags. no. Use diagonal optimizations. Faster, especially for closely related
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