mafft

TLDR

Align sequences (auto strategy)

$ mafft --auto [input.fasta] > [aligned.fasta]

Fast alignment

$ mafft --retree 1 [input.fasta] > [aligned.fasta]

Accurate alignment

$ mafft --maxiterate 1000 --localpair [input.fasta] > [aligned.fasta]

Use multiple threads

$ mafft --thread [8] --auto [input.fasta] > [aligned.fasta]

Add sequences to existing alignment

$ mafft --add [new.fasta] [existing.fasta] > [combined.fasta]

SYNOPSIS

mafft [options] input > output

MAFFT (Multiple Alignment using Fast Fourier Transform) is a high-performance multiple sequence alignment program. It offers various algorithms balancing speed and accuracy.
MAFFT is widely used in bioinformatics for aligning DNA, RNA, and protein sequences.

PARAMETERS

--auto

Auto-select strategy.

--maxiterate n

Number of iterations.

--localpair

Use L-INS-i (accurate).

--globalpair

Use G-INS-i.

--thread n

Number of threads.

--add file

Add to alignment.

--reorder

Reorder by similarity.

--quiet

Suppress messages.

STRATEGIES

$ FFT-NS-1  - Fast, large datasets
FFT-NS-2  - Default progressive
L-INS-i   - Accurate, <200 sequences
G-INS-i   - Global alignment

CAVEATS

Memory scales with sequence count. Very long sequences may need adjustments. Auto mode selects strategy based on input size.

HISTORY

MAFFT was developed by Kazutaka Katoh and colleagues, first published in 2002. It's one of the most cited alignment tools in bioinformatics.