aLeaves

aLeaves collects homologous sequences from diverse animal genomes to support molecular phylogenetic and comparative genomic analyses.

Key Features:

• Homolog collection: Retrieves sequences similar to an input query from multiple animal genome data sources to assemble candidate homologs for downstream analysis.
• Orthology identification: Uses explicit phylogenetic inference as the basis for identifying orthologs and distinguishing paralogs.
• Integration with MAFFT: Connects to the MAFFT multiple sequence alignment server to perform sequence alignments used for tree construction.
• Sequence selection (Archaeopteryx): Supports sequence selection based on tree visualization using the Archaeopteryx tree viewer.
• Iterative workflow: Enables iterative loops of sequence selection, alignment, and phylogenetic tree inference to refine datasets, reduce redundancy, and optimize taxon coverage.
• Data aggregation: Consolidates genomic sequences from multiple independent resources into a single collection for search and retrieval.

Scientific Applications:

• Molecular phylogenetics: Facilitates collection and phylogenetic analysis of homologous sequences to infer evolutionary relationships.
• Comparative genomics: Aids identification of orthologs and paralogs across animal genomes for comparative gene and genome studies.
• Zoology and evolutionary biology: Supports analyses of gene conservation, divergence, and species-level evolutionary questions across taxa.

Methodology:

Collects sequences similar to an input query from multiple data sources, performs multiple sequence alignment via MAFFT, constructs phylogenetic trees for explicit phylogenetic inference used in orthology identification, and supports iterative cycles of sequence selection, alignment, and tree inference.