Wasabi

Wasabi provides integrated visualization and analysis of multiple sequence alignments (MSAs) together with phylogenetic trees to support evolutionary sequence analysis.

Key Features:

• MSA and tree visualization: Visualizes multiple sequence alignments alongside phylogenetic trees for joint inspection of sequence and phylogenetic information.
• Ancestral sequence display: Displays reconstructed ancestral sequences at specific tree nodes.
• Phylogeny-aware alignment support: Supports PRANK and PAGAN for phylogeny-aware alignment and alignment extension.
• Ensembl integration: Imports sequence data, GeneTrees, and EPO alignments directly from Ensembl.
• Reproducibility: Automatically stores intermediate analysis steps to preserve analysis provenance.
• Data import: Accepts local files and remote URLs for sequence and alignment data input.
• Extensibility: Modular design enables integration with other bioinformatics tools.

Scientific Applications:

• Comparative genomics: Facilitates comparative genomics analyses using MSAs and Ensembl GeneTrees/EPO alignments.
• Gene evolution: Supports studies of gene evolution and lineage-specific sequence changes.
• Ancestral sequence reconstruction: Enables reconstruction and inspection of ancestral sequences at tree nodes.
• Evolutionary biology and genomics research: Supports phylogenetic and alignment-based analyses in evolutionary biology, genomics, and bioinformatics.

Methodology:

Visualizes MSAs with phylogenetic trees and ancestral sequences, supports PRANK and PAGAN for phylogeny-aware alignment and alignment extension, imports GeneTrees and EPO alignments from Ensembl, and records intermediate analysis steps.