Clustal WS (jabaws)

Clustal WS (jabaws) performs multiple sequence alignment of nucleic acid and protein sequences by integrating ClustalW and additional MSA algorithms within the JABAWS web services framework.

Key Features:

• Multiple Sequence Alignment Methods: Supports ProbCons, T-Coffee, Muscle, MAFFT, and ClustalW for diverse MSA strategies.
• Web Services Framework: Exposes MSA programs via the JABAWS web services framework for remote execution and integration.
• Flexible Deployment Options: Deliverable as a Virtual Appliance (VA) and Web Application Archive (WAR) and runnable on single machines or clusters managed by queuing systems such as Grid Engine or LSF with DRMAA support.
• Parameter Customization: Provides full access to each application's parameters via JABAWS:MSA with named parameter presets and execution limits configurable through simple configuration files.
• Integration Capabilities: Includes a command-line client for incorporation into scripts, automation, and batch processing.

Scientific Applications:

• Jalview integration: Integrated with the Jalview multiple sequence analysis workbench (since version 2.6) for MSA-driven analyses.
• Evolutionary studies: Produces global alignments for phylogenetic and comparative genomics analyses.
• Structural biology: Provides alignments to inform structure–function and conserved residue analyses.
• Functional genomics: Supports detection of conserved motifs and annotation of sequence function through accurate alignments.

Methodology:

Uses the ClustalW algorithm to perform global alignments by pairwise comparisons to build a guide tree that directs progressive alignment; integrated with JABAWS for scalable, configurable execution.