Simple Phylogeny (EBI)

Simple Phylogeny (EBI) generates phylogenetic trees from multiple sequence alignments using ClustalW2 to infer evolutionary relationships among biological sequences.

Key Features:

• Phylogenetic Tree Construction: Builds phylogenetic trees from sequence alignments using ClustalW2.
• Multiple Sequence Alignment: Performs multiple sequence alignment with ClustalW2 (Clustal W / Clustal X codebase) as the basis for tree inference.
• C++ Implementation: Clustal W and Clustal X have been rewritten in C++ to improve performance and provide compatibility with Linux, Macintosh, and Windows.
• EMBL-EBI Job Dispatcher Integration: Integrated into the EMBL-EBI Job Dispatcher framework and supports RESTful and SOAP-based APIs for programmatic job submission and retrieval.

Scientific Applications:

• Evolutionary Biology: Infers evolutionary relationships among genes, proteins, or taxa from aligned sequences.
• Comparative Genomics: Supports comparative analyses by providing phylogenetic context for genome-scale or gene-family studies.
• Molecular Phylogenetics: Reconstructs phylogenies for studying lineage diversification and the genetic basis of phenotypic traits across species.

Methodology:

Multiple sequence alignment is performed using ClustalW2, followed by phylogenetic tree construction; Clustal W and Clustal X are implemented in C++ and the tool integrates with the EMBL-EBI Job Dispatcher with RESTful and SOAP APIs.