MUSCLE 3.7 (doc)

Upload your set of sequences in FASTA, EMBL or NEXUS format from a file:

Or paste it here (load example of sequences)

Maximum number of sequences is 200 for proteins and 200 for nucleic acids.
Maximum length of sequences is 2000 for proteins and 6000 for nucleic acids.

Names associationOptionally, you can specify the association between truncated taxon names (used in input data) and original long taxon names (human readable). Each short name of a line on the left will be associated to the long name of the corresponding line on the right.
Note: line numbers leading each line will be automatically removed, don't worry about them.

Short names used in input dataShort names are the names used in the input data. Usually, theses names are short and only contain valid characters (no spaces, quotes and such).
Note: a short name must be associated to one and only one long name.
Real long names (human readable)Long names are explicit taxon names with unlimited length and can contain special characters.

Advanced Settings...

MUSCLE run mode (!)Click here for details.:
Full modeIncludes:
-stage 1: draft progressive alignment
-stage 2: improved progressive alignment
-stage 3: alignment refinement

Progressive mode (faster)Includes:
-stage 1: draft progressive alignment
-stage 2: improved progressive alignment

Fastest modeIncludes:
-stage 1: draft progressive alignment using the fastest possible options

Default/custom modeUse default/custom settings

Note: parameters are adjusted according to the selected running mode

Maximum number of iterationsYou can control the number of iterations that MUSCLE does. If you specify 1, 2 or 3, then this is exactly the number of iterations that will be performed. If the value is greater than 3, then MUSCLE will continue up to the maximum you specify or until convergence is reached, which ever happens sooner. The default is 16. If you have a large number of sequences, curation may be rather slow.: (default: 16)
Find diagonalsCreating a pair-wise alignment by dynamic programming requires computing an L1 × L2 matrix, where L1 and L2 are the sequence lengths. A trick used in algorithms such as BLAST is to reduce the size of this matrix by using fast methods to find diagonals, i.e. short regions of high similarity between the two sequences. This speeds up the algorithm at the expense of some reduction in accuracy. MUSCLE uses a technique called k-mer extension to find diagonals. (faster for similar sequences)

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