Issue Description

Vendor the MAFFT (Multiple Alignment using Fast Fourier Transform) tool into the DeepCritical bioinformatics MCP server ecosystem. This tool performs multiple sequence alignment of biological sequences.

Biological Context

MAFFT is one of the most widely used tools for multiple sequence alignment in bioinformatics. It uses advanced algorithms including Fast Fourier Transform to achieve high accuracy and speed. MAFFT is essential for comparative genomics, phylogenetic analysis, and understanding sequence conservation and variation.

Data Details

• Tool: MAFFT (Multiple sequence alignment)
• Input: Multi-FASTA files with biological sequences
• Output: Aligned sequences in various formats
• Container: biocontainers/mafft
• Use Cases: Protein family analysis, phylogenetic studies, conserved region identification

Command Used

# Example MAFFT commands
mafft input.fasta > aligned.fasta                    # Auto-select algorithm
mafft --auto input.fasta > aligned.fasta            # Automatic algorithm selection
mafft --localpair --maxiterate 1000 input.fasta > aligned.fasta  # L-INS-i method

Bioinformatics Configuration

# Tool configuration
mafft:
  enabled: true
  container: "biocontainers/mafft:latest"
  default_params:
    auto: true
    maxiterate: 1000
    localpair: false
    globalpair: false
  supported_formats: ["fasta", "clustal", "phylip"]

Expected Results

• MCP server with @mcp_tool decorated mafft function
• Support for different MAFFT algorithms (FFT-NS-1, FFT-NS-2, L-INS-i, etc.)
• Multiple output format options
• Proper handling of large sequence datasets

Actual Results

MAFFT is currently not implemented in the bioinformatics MCP server collection.

Scientific Impact

Without MAFFT, researchers cannot:

• Perform multiple sequence alignments for comparative analysis
• Identify conserved regions in protein families
• Build accurate phylogenetic trees
• Analyze sequence conservation and variation

This tool is fundamental for molecular evolution and comparative genomics studies.

Additional Context

The tool should support MAFFT's various algorithms optimized for different sequence types and sizes. Integration with downstream phylogenetic tools and proper handling of alignment quality metrics is important.