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muscle: multiple sequence alignment with high accuracy and high throughput

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Popular multiple alignment software. MUSCLE is one of the most widely-used methods in biology. On average, MUSCLE is cited by ten new papers every day. Fast, accurate and easy to use. MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and
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
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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