Summary

• Vendor the MAFFT (Multiple Alignment using Fast Fourier Transform) tool into the DeepCritical bioinformatics MCP server ecosystem
• Implement MAFFTServer class with 3 MCP tools: mafft_align, mafft_add, mafft_merge
• Support for multiple alignment algorithms (FFT-NS-1, FFT-NS-2, L-INS-i, G-INS-i, E-INS-i) with automatic selection
• Multiple output formats (FASTA, ClustalW, Phylip)
• Register MAFFT server in mcp_server_management.py and mcp_server_tools.py

Files Changed

• New: DeepResearch/src/tools/bioinformatics/mafft_server.py - MAFFT MCP server implementation
• New: docker/bioinformatics/Dockerfile.mafft - Docker container for MAFFT
• New: tests/test_bioinformatics_tools/test_mafft_server.py - 34 tests (all passing)
• Modified: DeepResearch/src/tools/mcp_server_management.py - Register MAFFTServer
• Modified: DeepResearch/src/tools/mcp_server_tools.py - Register MAFFTServer

Quality Checks

• ruff check: All checks passed
• ruff format: All files formatted
• ty check: All checks passed
• pytest: 34 passed, 1 skipped (containerized)

Test Plan

• Server initialization and configuration
• All 3 MCP tools listed (align, add, merge)
• Align with auto, L-INS-i, G-INS-i, E-INS-i algorithms
• ClustalW output format support
• Add sequences to existing alignment (add, addfragments)
• Merge pre-aligned groups
• Input validation (missing files, invalid algorithms, invalid formats, etc.)
• Mock functionality when MAFFT binary not available
• Error handling for invalid/missing operations

Closes #138

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