mafft

name	mafft
description	Use when performing multiple sequence alignment on nucleotide or protein sequences, such as preparing alignments for phylogenetic analysis or comparative genomics.
disable-model-invocation	true
user-invocable	true

mafft

Quick Start

• Command: mafft [options] input.fasta > output.fasta
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/mafft
• Version: 7.526
• Full reference: See references/help.md for complete options and documentation

When To Use This Tool

• Build a multiple-sequence alignment for nucleotide or protein FASTA input.
• Use it before phylogenetic inference, motif comparison, or profile building.
• Start with --auto when you are unsure which alignment strategy fits the dataset.
• Switch to high-accuracy iterative modes for smaller, harder alignments.

Common Patterns

# 1) Let MAFFT choose the strategy
mafft --auto input.fasta > aligned.fasta

# 2) High-accuracy local-pair alignment
mafft --maxiterate 1000 --localpair input.fasta > aligned.fasta

# 3) Use all available threads
mafft --auto --thread -1 input.fasta > aligned.fasta

# 4) Output CLUSTAL format
mafft --auto --clustalout input.fasta > aligned.aln

Recommended Workflow

1. Check that the input sequences are homologous enough to align meaningfully.
2. Start with --auto unless you already know the dataset requires a specific mode.
3. Move to --localpair or related high-accuracy modes only for smaller, biologically difficult alignments.
4. Inspect the alignment before sending it to iqtree, hmmbuild, or downstream comparative analyses.

Guardrails

• High-accuracy iterative modes are not the default answer for large datasets.
• The MAFFT help text explicitly suggests the expensive iterative modes mainly for smaller inputs.
• Changing --op and --ep without a biological reason can degrade alignments quickly.
• MAFFT writes alignment to stdout by default, so remember shell redirection.