ORTHOSCOPE

ORTHOSCOPE infers orthologous gene groups and reconstructs gene trees to support phylogenetic inference among bilaterian species.

Key Features:

• Integration of Genomic Data: Integrates over 250 metazoan gene models predicted from various genome projects to provide a comprehensive dataset for analysis.
• User-Defined Taxonomic Sampling: Supports user-defined taxonomic sampling and input of specific sequence molecules to tailor taxon sampling for orthogroup inference.
• Gene Tree Estimation: Estimates gene trees for candidate genes across major bilaterian lineages.
• Species Tree Comparison: Compares estimated gene trees with a user-specified species tree to refine orthogroup identification.
• Reliability Evaluation: Evaluates the reliability of inferred orthogroups using gene tree topologies and node support values.
• Efficiency and Scale: Completed a test analysis using data from 36 bilaterian species in approximately 140 seconds, demonstrating capacity for genome-scale datasets.
• Comparative Analysis: Produces results usable to evaluate orthologs identified by other stand-alone programs that utilize genome-scale data.

Scientific Applications:

• Evolutionary relationships: Infers evolutionary relationships among bilaterian species for studies in evolutionary biology and genomics.
• Gene evolutionary history: Provides insights into gene function conservation, divergence, and the evolutionary history of genes across diverse lineages.
• Phylogenetic reconstruction: Supports studies aiming to unravel complex phylogenetic relationships within Metazoa.
• Comparative genomics and benchmarking: Serves as a resource for comparative genomic studies and for evaluating orthology inferences from other genome-scale tools.

Methodology:

Estimates gene trees and compares them with a species tree, incorporates user-defined taxonomic sampling, and evaluates reliability using gene-tree topologies and node support values.