TaxOnTree

TaxOnTree annotates phylogenetic trees with taxonomic information to enable interpretation of evolutionary relationships among genes, proteins, and species.

Key Features:

• Input Flexibility: Accepts a single phylogenetic tree in Newick format containing gene/protein identifiers from NCBI or Uniprot, protein identifiers, individual proteins in FASTA format, lists of protein accessions, and (un)aligned multi-FASTA files.
• Phylogenetic Reconstruction: Includes a built-in phylogenetic reconstruction pipeline to generate trees from non-tree inputs.
• Taxonomic Annotation: Retrieves taxonomic information via web requests to NCBI or Uniprot servers or from a local MySQL database and annotates tree nodes with taxonomic tags.
• Output Format: Produces a Nexus format tree file compatible with FigTree and supports branch coloring and tip/node labeling based on the incorporated taxonomic information.

Scientific Applications:

• Enhanced Visualization: Visualizing taxonomic context on phylogenetic trees via branch coloring and tip/node labels.
• Orthologs and Paralogs Inspection: Examining the taxonomic distribution of orthologous and paralogous sequences to study gene evolution and function across species.
• Manual Curation Support: Supporting manual curation of taxonomic and phylogenetic scenarios.
• Integration with Other Tools: Coupling with tools that link homologous sequences to a seed sequence for extended genomic analyses.

Methodology:

Accepts diverse input formats and reconstructs phylogenetic trees when required; retrieves taxonomic data via web requests to NCBI or Uniprot servers or from a local MySQL database; and annotates tree nodes with this taxonomic information, exporting the annotated tree in Nexus format.