MultipleSequenceAlignment HowTo

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MAFFT

$ mafft [options] input.fa > out.aln

Options for algorithms:

  • --auto : to choose either fast, less accurate algorithm, or slow, more accurate one.
  • --6merpair : the distance is calculated based on the number of shared 6mers. (default)
  • --globalpair : using the Needleman-Wunsch algorithm
  • --localpair : using the Smith-Waterman algorithm
  • --genafpair : local alignment with generalized affine gap cost

Options for output:

  • --distout : to generate distance matrix (.hat2 file) (ref)
  • --clustalout : clustal format (default is fasta format)
  • --treeout : guide tree

References

MUSCLE

CLUSTAL-OMEGA

CD-HIT