Table 1.
Options of MAFFT Version 7.
| Option name | Command | |
|---|---|---|
| For a large-scale alignment: progressive methods with the PartTree algorithm | ||
| NW-NS-PartTree1 | mafft ––parttree ––retree 1 input | Distance is by the 6mer method. |
| NW-NS-PartTree2 | mafft ––parttree ––retree 2 input | Distance is by the 6mer method. Guide tree is re-built. |
| NW-NS-DPPartTree1 | mafft ––dpparttree ––retree 1 input | Distance is estimated based on DP. |
| NW-NS-DPPartTree2 | mafft ––dpparttree ––retree 2 input | Distance is estimated based on DP. Guide tree is re-built. |
| For a medium-scale alignment: progressive methods | ||
| FFT-NS-1 | mafft ––retree 1 input | Approximately two times faster than the default. |
| FFT-NS-2 | mafft input | Default. |
| For a small-scale alignment: iterative refinement methods | ||
| FFT-NS-i | mafft ––maxiterate 16 input | Fastest of the four in this category. Uses WSP score (Gotoh 1995) only. |
| G-INS-i | mafft ––maxiterate 16 ––globalpair input | Uses WSP score and consistency (Notredame et al. 1998) score from global alignments. |
| L-INS-i | mafft ––maxiterate 16 ––localpair input | Uses WSP score and consistency score from local alignments. |
| E-INS-i | mafft ––maxiterate 16 ––genafpair input | Uses WSP score and consistency score from local alignments with a generalized affine gap cost (Altschul 1998). |
| If not sure which option to use | ||
| Automatic | mafft ––auto | Selects an appropriate option from FFT-NS-2, FFT-NS-i and L-INS-i, according to the size of input data. |
| For a small-scale RNA alignment: structural alignment methods | ||
| Q-INS-i | mafft-qinsi input | Structure information is included in iterative refinement step. |
| X-INS-i-scarnapair | mafft-xinsi ––scarnapair input | Uses pairwise structural alignment by MXSCARNA (Tabei et al. 2008). |
| To add new sequences into an existing MSA | ||
| Add | mafft ––add mew msa | The simplest option for alignment extension. |
| Addprofile | mafft ––addprofile msa1 msa2 | msa1 must form a monophyletic cluster. |
| Addfragments | mafft ––addfragments new msa | Suitable for short new sequences. |
| Addfragments, LAST | mafft ––addfragments new ––lastmultipair msa | Faster option, LAST (Kiełbasa et al. 2011) is required. |
| Addfragments, 6mer | mafft ––addfragments new ––6merpair msa | Faster option for conserved data. |
| Parameters | ||
| ––bl #, ––jtt #, ––tm # | Score matrices for protein alignment. | |
| ––kimura # | Score matrix for nucleotide alignment. | |
| Utility options | ||
| ––anysymbol | See main text. | |
| ––reorder | ||
| ––clustalout | ||
| ––phylipout | ||
| ––namelength # | ||
| ––adjustdirection | ||
| ––adjustdirectionaccurately | ||
| ––seed msa1 –seed msa2 … | ||
| ––treein treefile | ||
| ––treeout | ||
| ––thread # | ||
Note.—N, the number of sequences; L, the sequence length; input, new, unaligned sequences in the multi-fasta format; msa, msa1, msa2, aligned sequences in the multi-fasta format; treefile, input guide tree file.