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 |
| Fast | Progressive | N/A | fft-ns-2 |
| Very fast | Progressive | > 2000 | fft-ns-1 |
- in the Scoring matrix drop-down menu, choose the desired matrix:
| Matrix name | Description |
|---|---|
| Nucleotide sequences | |
| 1PAM / k=2 | For closely related sequences. |
| 20PAM / k=2 | For moderately related sequences. |
| 200 PAM / k=2 | For distantly related sequences. |
| Protein 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.
Need more help with this?
Contact DNASTAR