MAFCO

MAFCO compresses MAF (Multiple Alignment Format) files using a lossless algorithm optimized for whole-genome multiple alignments to reduce storage footprint while preserving alignment data integrity.

Key Features:

• Lossless compression: Implements a lossless algorithm specifically tailored for MAF files to preserve all alignment information.
• MAF specialization: Targets MAF files that contain alignments between entire genomes across multiple species.
• Compression performance vs gzip: Achieves compression gains ranging from 34% to 57% compared to gzip depending on the dataset.
• Improvement over dedicated methods: Reports an average 9% compression improvement relative to other dedicated methods on compatible datasets.

Scientific Applications:

• Archival storage of whole-genome alignments: Reduces storage requirements for MAF files generated in whole-genome comparative analyses.
• Management of large comparative genomics datasets: Facilitates handling and long-term retention of large multiple-alignment datasets without data loss.
• Preservation for downstream analyses: Maintains complete alignment information for subsequent comparative genomics and evolutionary analyses.

Methodology:

Uses a lossless compression algorithm tailored to MAF (Multiple Alignment Format) files and evaluates performance against gzip and other dedicated compression methods.