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Flag option
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Set by default?
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Description
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anchors
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yes
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Use anchor optimization in tree dependent refinement iterations.
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brenner
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no
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Use Steven Brenner's method for computing the root alignment.
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cluster
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no
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Perform fast clustering of input sequences. Use the – tree1 option to save the tree.
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dimer
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no
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Use dimer approximation for the SP score (faster, slightly less accurate).
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clw
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no
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Write output in CLUSTALW format (default is FASTA).
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clwstrict
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no
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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.
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core
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yes in muscle,
no in muscled.
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Do not catch exceptions.
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diags
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no
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Use diagonal optimizations. Faster, especially for closely related sequences, but may be less accurate.
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diags1
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no
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Use diagonal optimizations in first iteration.
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diags2
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no
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Use diagonal optimizations in second iteration.
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fasta
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yes
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Write output in FASTA format.
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group
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yes
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Group similar sequences together in the output. This is the default. See also – stable .
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html
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no
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Write output in HTML format (default is FASTA).
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le
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maybe
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Use log-expectation profile score (VTML240). Alternatives are to use – sp or –sv . This is the default for amino acid sequences.
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msf
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no
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Write output in MSF format (default is FASTA). Designed to be compatible with the GCG package.
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noanchors
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no
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Disable anchor optimization. Default is – anchors .
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nocore
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no in muscle,
yes in muscled.
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Catch exceptions and give an error message if possible.
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phyi
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no
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Write output in Phylip interleaved format.
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phys
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no
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Write output in Phylip sequential format.
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profile
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no
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Compute profile-profile alignment. Input alignments must be given using – in1 and – in2 options.
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quiet
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no
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Do not display progress messages.
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refine
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no
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Input file is already aligned, skip first two iterations and begin tree dependent refinement.
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refinew
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no
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Refine an alignment by dividing it into non-overlapping windows and re-aligning each window. Typically used for whole-genome nucleotide alignments.
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sp
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no
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Use sum-of-pairs protein profile score (PAM200). Default is – le.
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spscore
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no
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Compute alignment score of profile-profile alignment. Input alignments must be given using – in1 and – in2 options. These must be pre-aligned with gapped columns as needed, i.e. must be of the same length (have same number of columns).
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spn
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maybe
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Use sum-of-pairs nucleotide profile score. This is the only option for nucleotides, and is therefore the default. The substitution scores and gap penalty scores are "borrowed" from BLASTZ.
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stable
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no
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Preserve input order of sequences in output file. Default is to group sequences by similarity (– group ).
WARNING THIS OPTION WAS BUGGY AND IS NOT SUPPORTED IN v3.8. Go to this link for more information: /muscle/manual/stable.html
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sv
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no
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Use sum-of-pairs profile score (VTML240). Default is – le.
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termgaps4
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yes
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Use 4-way test for treatment of terminal gaps. (Cannot be disabled in this version).
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termgapsfull
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no
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Terminal gaps penalized with full penalty.
[1] Not fully supported in this version.
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termgapshalf
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yes
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Terminal gaps penalized with half penalty.
[1] Not fully supported in this version.
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termgapshalflonger
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no
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Terminal gaps penalized with half penalty if gap relative to
longer sequence, otherwise with full penalty.
[1] Not fully supported in this version.
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verbose
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no
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Write parameter settings and progress messages to log file.
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version
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no
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Write version string to stdout and exit.
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