MAFFT Sequence Alignment: Default Settings and Output

Yes, you can perform a sequence alignment using MAFFT without using any specific options. By default, MAFFT uses the 'auto' option, which selects the appropriate algorithm and other parameters based on the input sequence length and type. So, the command 'mafft example.fasta > results.fasta' will perform a sequence alignment using the default settings and save the results in the 'results.fasta' file.