The MAFFT algorithm is for gene level alignment of either protein or nucleotide sequences. To run a MAFFT alignment, select two or more sequences and choose Align > (Re)Align Using MAFFT.
If you wish to change method options, instead choose Align > Align with Options. Options vary depending whether the sequences are protein or nucleotide (nucleotide version shown below).
Change settings as desired:
- Use the Align drop-down menu to select sequences to align or realign.
- In the Using drop-down menu, choose Clustal W.
- Specify the Gap open penalty, the numerical penalty for introducing a gap of any length when calculating alignments. This penalty does not take into account the size of the gap. The default is -2.0.
- Gap extension penalty – This option affects the lengths of gaps, and must be zero or a negative number. Lowering the magnitude of the gap extension penalty may allow for longer gaps. The default is 0.
- In the Algorithm drop-down menu, either retain the default of Choose algorithm depending upon size [auto], or specify a particular alignment algorithm.
|Description||Name||No. of Seqs||Strategy|
|Choose algorithm depending upon size [auto]||(default)|
|Very slow||global homology||< 200||g-ins-i|
|Very slow||one conserved domain||< 200||l-ins-i|
|Very slow||multiple conserved domains||< 200||e-ins-i|
|Slow||iterative refinement, iterations specified by user||N/A||fft-ns-i|
|Medium||Iterative refinement, two iterations||N/A||N/A|
|Very fast||Progressive||> 2000||fft-ns-1|
- in the Scoring matrix drop-down menu, choose the desired matrix:
|1PAM / k=2||For closely related sequences.|
|20PAM / k=2||For moderately related sequences.|
|200 PAM / k=2||For distantly related sequences.|
|BLOSUM30, 45, 62, 80||(Henikoff & Henikoff, 1992). The BLOSUM series of matrices contain the same values as in some of MegAlign Pro’s other alignment methods, except that the protein ambiguity codes B, Z, and X are excluded in this case. These matrices are ideal for carrying out similarity searches. Choose a larger number BLOSUM matrix for less divergent sequences.|
|JTT100, 200||(Thorne JL et al., 1998) These matrices are similar to PAM matrices and were generated using an algorithm similar to the approach of Dayhoff et al. (1978), but based on a larger set of protein sequences.|
After making your changes:
- Choose Align to use the entered options to perform a multiple sequence alignment.
- Use the Reset to Default button if you would like to reset all values to the MegAlign Pro defaults.
- Select Cancel to leave the dialog without saving any changes.
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