Multiple Alignment

Flag optionSet by default?Description
anchorsyesUse anchor optimization in tree dependent refinement iterations.
brennernoUse Steven Brenner's method for computing the root alignment.
clusternoPerform fast clustering of input sequences. Use the –tree1 option to save the tree.
dimernoUse dimer approximation for the SP score (faster, slightly less accurate).
clwnoWrite output in CLUSTALW format (default is FASTA).
clwstrictnoWrite 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.
coreyes in muscle,no in muscled.Do not catch exceptions.
diagsnoUse diagonal optimizations. Faster, especially for closely related sequences, but may be less accurate.
diags1noUse diagonal optimizations in first iteration.
diags2noUse diagonal optimizations in second iteration.
fastayesWrite output in FASTA format.
groupyesGroup similar sequences together in the output. This is the default. See also –stable.
htmlnoWrite output in HTML format (default is FASTA).
lemaybeUse log-expectation profile score (VTML240). Alternatives are to use –sp or –sv. This is the default for amino acid sequences.
msfnoWrite output in MSF format (default is FASTA). Designed to be compatible with the GCG package.
noanchorsnoDisable anchor optimization. Default is –anchors.
nocoreno in muscle,yes in muscled.Catch exceptions and give an error message if possible.
phyinoWrite output in Phylip interleaved format.
physnoWrite output in Phylip sequential format.
profilenoCompute profile-profile alignment. Input alignments must be given using –in  and –in2 options.
quietnoDo not display progress messages.
refinenoInput file is already aligned, skip first two iterations and begin tree dependent refinement.
refinewnoRefine an alignment by dividing it into non-overlapping windows and re-aligning each window. Typically used for whole-genome nucleotide alignments.
spnoUse sum-of-pairs protein profile score (PAM200). Default is –le.
spscorenoCompute 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).
spnmaybeUse 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.
stablenoPreserve 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
svnoUse sum-of-pairs profile score (VTML240). Default is –le.
termgaps4yesUse 4-way test for treatment of terminal gaps. (Cannot be disabled in this version).
termgapsfullnoTerminal gaps penalized with full penalty. [1] Not fully supported in this version.
termgapshalfyesTerminal gaps penalized with half penalty. [1] Not fully supported in this version.
termgapshalflongernoTerminal gaps penalized with half penalty if gap relative to longer sequence, otherwise with full penalty. [1] Not fully supported in this version.
verbosenoWrite parameter settings and progress messages to log file.
versionnoWrite version string to stdout and exit.

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