Cactus

Cactus performs reference-free whole-genome multiple alignment to compare tens to thousands of genome assemblies (including vertebrate and amniote genomes) and to identify small polymorphisms, complex structural variations, rearrangements, and duplications for comparative and evolutionary genomics.

Key Features:

• Reference-Free Alignment: Performs multiple alignments without relying on a single reference genome, enabling direct comparisons across diverse species.
• Handling Complex Variations: Captures small polymorphisms as well as complex structural variations, including large-scale rearrangements and copy number variations.
• Cactus Graphs: Uses cactus graphs to represent duplications and general genomic rearrangements, decomposing common substructures into hierarchical chains for multiple-alignment representation and circular genome plots.
• Scalability: Implements Progressive Cactus to scale alignments to hundreds of genomes, demonstrated on alignments of over 600 amniote genomes.
• Performance and Accuracy: Demonstrates improved accuracy and efficiency in empirical assessments using the Evolver genome evolution simulator and effectively aligns genes and intra-gene duplications, particularly within primate genomes.

Scientific Applications:

• Genome Evolution Studies: Enables study of genome evolution and evolutionary relationships across species by providing reference-free alignments.
• Structural Variation Analysis: Supports analysis of structural genomics by resolving rearrangements and copy number variations relevant to genetic diversity and disease.
• Comparative Genomics: Facilitates comprehensive comparative genomic analyses across wide taxonomic ranges, including vertebrates and amniotes.

Methodology:

Employs cactus graphs that decompose common substructures into hierarchical chains to represent duplications and rearrangements, uses Progressive Cactus for scalable progressive alignment, and has been empirically assessed using the Evolver genome evolution simulator.