MAFFT HELP
MAFFT main parameters
- Sequence Format
-
Fasta: A common sequence format offered by most sequence and alignment editors.
- Format: A 'greater than' symbol followed by the sequence name. The following line is the sequence.
- Example:
- >MCIN08472-PA
- MKALQCRSGNQQTSDELRKIMEKCNRHQSNGKHDDDSSVDDSSDNSSEEVMFSRDFFTSSKKSSENTTKNPRNSFASSGMYSSDQYR
- RQFGNKPFDMSHSDYSGFQQNSRISDSSNKNDQKSDENQRNSCNIQCFFDELNLVDQRGFPERIAVTKTMLKNIQYPDLRDFVEESILECF
- QFLTNNSNQDKCEFSQNLVNCFADKGKEGCEDWDG
- OUTPUT
-
Format for generated multiple sequence alignment.
- Pearson/FASTA: Pearson or FASTA sequence format.
- ClustalW: ClustalW alignment format without base/residue numbering.
- Default value is: Pearson/FASTA [fasta]
- Upload
-
- A file containing three or more valid sequences in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot)
- can be uploaded and used as input for the multiple sequence alignment. Word processor files may yield unpredictable results as
- hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters.
- There is currently a file upload limit of 500 sequences and 1MB of data.
-
- Matrix
-
Protein comparison matrix to be used when adding sequences to the alignment.
- Matrix (Protein Only)>>>>>>Abbreviation
- BLOSUM30>>>>>>bl30
- BLOSUM45>>>>>>bl45
- BLOSUM62>>>>>>bl62
- BLOSUM80>>>>>>bl80
- JTT PAM100>>>>>>jtt100
- JTT PAM200>>>>>>jtt200
- Default value is: BLOSUM62 [bl62]
- Gap Open
-
Penalty for first base/residue in a gap.
- Default value is: 1.53
- Gap Extension
-
Penalty for each additional base/residue in a gap.
- Default value is: 0.123
- Order
-
The order in which the sequences appear in the final alignment
- Order>>>Description>>>Abbreviation
- aligned>>>Determined by the guide tree>>>aligned
- input>>>Same order as the input sequences>>>input
- Default value is: aligned
- Tree Rebuilding Number
-
Default value is: 2
- Guide OUTPUT
-
Generate guide tree file
- Default value is: ON [true]
- Max Iterate
-
Maximum number of iterations to perform when refining the alignment
- Default value is: 2
- Perform FFTS
-
Perform fast fourier transform
- none
- localpair
- genafpair
- globalpair
- Default value is: none