ORTHOSCOPE

ORTHOSCOPE is a web-based tool designed for accurately identifying orthologous and paralogous relationships among coding genes in comparative genomics. Particularly useful for deeply diversified bilaterian lineages, the tool relies on precise gene tree estimation to navigate the complex evolutionary histories of genes spanning millions of years. It achieves ortholog identification through the concept of orthogroups—sets of genes descending from a single gene in the last common ancestor of the species under consideration. By integrating over 250 metazoan gene models from genome projects, ORTHOSCOPE addresses the challenge of scattered genomic data across various web databases. The tool allows users to query specific protein-coding genes using sequences and well-accepted nodes from a user-defined species tree. It assesses the reliability of orthogroup estimations based on gene tree topologies and support values of nodes. ORTHOSCOPE's efficiency is demonstrated through a test analysis involving 36 bilaterian organisms completed in a short time frame. The resulting data can be used to validate orthologs identified by other standalone programs employing genome-scale data.