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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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The primary output is specified using the -out option, and defaults to standard output. Multiple output formats in one run. You can specify several -xxxout option on the same command line, which allows you to create multiple output formats in a single run, e.g.: muscle -in seqs.fa -fastaout seqs.afa -clwout seqs.aln
MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that gave the best average benchmark accuracy in my tests. However,.
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