Multiple alignment program for amino acid or nucleotide sequences

Supported in versions 6.840 and higher

Uppercase/lowrecase

When the --preservecase option is given, uppercase/lowercase is preserved as in the input file.

% mafft --preservecase input > output

When the input data is:

>
SAMPLEsequenCE1
>
samplSEQUENCE2
>
SampleSequenCE3

With --preservecase, the result is:

>
SAMPLEsequenCE1
>
sampl-SEQUENCE2
>
SampleSequenCE3

The --preservecase option is internally equivalent to the --anysymbol option.  Unusual symbols (O, U, @, #, 1, 2, etc) are also accepted.

Without --preservecase or --anysymbol, amino acid sequeces are converted to uppercase, and nucleotide sequences are converted to lowercase.  Non-alphabetical characters are deleted.

>
SAMPLESEQUENCE
>
SAMPL-SEQUENCE
>
SAMPLESEQUENCE