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Important note: This tool can align up to 500 sequences or a maximum file size of 1 MB. STEP 1 - Enter your input sequences. Enter or paste a set of sequences This manual page documents briefly the muscle command. muscle aligns protein sequences and is considered superior and faster than Clustal W. 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 MUSCLE. A program to create multiple sequence alignments of a large number of sequences. Documentation: drive5.com/muscle/manual/ Input files for profile-profile alignment, i.e. to align two multiple alignments to each other. Aligned FASTA format. -profile, Perform profile-profile An example of the Hammerhead ribozyme MUSCLE alignment versus the manually On average, alignments in which the manual curation affected a greater number 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 Description MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences. biocViews MultipleSequenceAlignment, Alignment, Sequencing, Description MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences. biocViews MultipleSequenceAlignment, Alignment, Sequencing, Tools for manual alignment; Tools for automated alignment; Various statistics about taxa except that it works for Robert C. Edgar's MUSCLE program.