MAFFT (EBI)

MAFFT (EBI) performs high-speed multiple sequence alignment of nucleotide and protein sequences for comparative and phylogenetic analyses.

Key Features:

• Add unaligned sequences: Options for adding unaligned sequences into an existing alignment are provided to incorporate new sequences without re-aligning the entire dataset.
• Adjust nucleotide direction: Functionality to adjust sequence direction in nucleotide alignments handles reverse-complement and strand-orientation issues.
• Constrained alignments: Support for constrained alignments allows portions of alignments to be fixed during optimization.
• Parallel processing: Parallel processing capabilities accelerate alignment computation for large datasets.
• EMBL-EBI Job Dispatcher integration: Integration with the EMBL-EBI Job Dispatcher framework connects MAFFT to EMBL-EBI services and workflows.
• Database integration: Integration with UniProt, InterPro, ENA, and Ensembl Genomes enables use of sequence data from these resources.
• API access: RESTful and SOAP-based API interfaces are available for programmatic submission and retrieval of jobs and results.
• Scalability: Updates to accommodate increased usage demonstrate support for large-scale sequence analysis demands.

Scientific Applications:

• Evolutionary biology: Multiple sequence alignments produced by MAFFT (EBI) support evolutionary inference and comparative sequence analyses.
• Phylogenetic analyses: Alignments are used as input for phylogenetic reconstruction and tree-based studies.
• Comparative genomics: MAFFT (EBI) facilitates sequence comparison across species and genomic regions for conservation and divergence analyses.
• Large-dataset processing: Parallel processing and scalability make the tool suitable for aligning large sequencing-derived datasets.

Methodology:

MAFFT (EBI) applies sophisticated sequence-alignment algorithms to achieve high accuracy and computational efficiency and supports parallel processing, adding unaligned sequences into existing alignments, adjusting nucleotide direction, and constrained alignments.