anchors

yes

Use anchor optimization in tree dependent refinement iterations.

brenner

no

Use Steven Brenner's method for computing the root alignment.

cluster

no

Perform fast clustering of input sequences. Use the –tree1 option to save the tree.

dimer

no

Use dimer approximation for the SP score (faster, slightly less accurate).

clw

no

Write output in CLUSTALW format (default is FASTA).

clwstrict

no

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 sequences, but may be less accurate.

diags1

no

Use diagonal optimizations in first iteration.

diags2

no

Use diagonal optimizations in second iteration.

fasta

yes

Write output in FASTA format.

group

yes

Group similar sequences together in the output. This is the default. See also –stable.

html

no

Write output in HTML format (default is FASTA).

le

maybe

Use log-expectation profile score (VTML240). Alternatives are to use –sp or –sv. This is the default for amino acid sequences.

msf

no

Write output in MSF format (default is FASTA). Designed to be compatible with the GCG package.

noanchors

no

Disable anchor optimization. Default is –anchors.

nocore

no in muscle,

yes in muscled.

Catch exceptions and give an error message if possible.

phyi

no

Write output in Phylip interleaved format.

phys

no

Write output in Phylip sequential format.

profile

no

Compute profile-profile alignment. Input alignments must be given using –in1 and –in2 options.

quiet

no

Do not display progress messages.

refine

no

Input file is already aligned, skip first two iterations and begin tree dependent refinement.

refinew

no

Refine an alignment by dividing it into non-overlapping windows and re-aligning each window. Typically used for whole-genome nucleotide alignments.

sp

no

Use sum-of-pairs protein profile score (PAM200). Default is –le.

spscore

no

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).

spn

maybe

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.

stable

no

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

sv

no

Use sum-of-pairs profile score (VTML240). Default is –le.

termgaps4

yes

Use 4-way test for treatment of terminal gaps. (Cannot be disabled in this version).

termgapsfull

no

Terminal gaps penalized with full penalty.

[1] Not fully supported in this version.

termgapshalf

yes

Terminal gaps penalized with half penalty.

[1] Not fully supported in this version.

termgapshalflonger

no

Terminal gaps penalized with half penalty if gap relative to

longer sequence, otherwise with full penalty.

[1] Not fully supported in this version.

verbose

no

Write parameter settings and progress messages to log file.

version

no

Write version string to stdout and exit.