Physcraper

Physcraper updates phylogenetic estimates by integrating new publicly available molecular sequence data into existing phylogenies to continually refine evolutionary hypotheses.

Key Features:

• Automated phylogeny updates: Incorporates new DNA sequences into established alignments and updates phylogenetic estimates automatically.
• Integration with Open Tree of Life: Utilizes Open Tree of Life resources to link taxonomic data across databases and compare original versus updated phylogenetic hypotheses.
• Public sequence integration: Leverages publicly available DNA sequences to expand and enhance previously published phylogenetic alignments.
• Molecular dataset assembly and topology comparison: Assembles molecular datasets and compares alternative phylogenetic topologies.
• Command-line Python implementation: Operates as a command-line Python program enabling scripted and reproducible phylogenetic updates.

Scientific Applications:

• Taxonomy: Updates phylogenies used for taxonomic revision and species-level hypotheses.
• Evolutionary biology: Refines evolutionary estimates and hypotheses by integrating new molecular data.
• Conservation genetics: Improves phylogenetic context for conservation assessments and genetic diversity studies.
• Phylogenetic research: Enables continual refinement of published phylogenies and comparison of competing topologies.

Methodology:

Retrieves and integrates publicly available DNA sequences into previously published alignments, links taxonomic data using Open Tree of Life resources, and automates phylogenetic reconstruction and topology comparison within a command-line Python workflow.