CIPRes

CIPRes provides programmatic access to computational resources for phylogenetic analysis and multiple sequence alignment on high-performance infrastructures.

Key Features:

• RESTful CRA: Exposes a RESTful application programmer interface (CRA) for programmatic interaction with the gateway's services.
• Phylogenetic and MSA codes: Hosts parallel tree inference and multiple sequence alignment codes for large-scale analyses.
• Integrated software: Executes MrBayes, BEAST, RAxML, and MAFFT via the gateway.
• High-performance execution: Runs analyses on XSEDE (NSF Extreme Science and Engineering Discovery Environment) computational resources.
• Programmatic access methods: CRA supports HTTP clients and scripting access, including curl and scripting languages, for integration into external applications.

Scientific Applications:

• Phylogenetic inference: Parallel tree inference for large datasets using MrBayes, RAxML, and BEAST.
• Multiple sequence alignment: Scalable multiple sequence alignment using MAFFT for downstream phylogenetic and comparative analyses.
• Integration with domain-specific databases: Incorporated into web resources such as Influenza Research Database (www.fludb.org), Virus Pathogen Resource (www.viprbrc.org), and MorphoBank (www.morphobank.org) to support virology and systematics research.

Methodology:

Implements a RESTful CRA that exposes execution of MrBayes, BEAST, RAxML, and MAFFT for parallel tree inference and multiple sequence alignment on XSEDE computational infrastructures, with access via HTTP clients such as curl and scripting languages.