https://chtsai0105.github.io/tags/orthology/OrthologyHugoBlox Kit (https://hugoblox.com)en-usWed, 12 Aug 2026 22:48:23 -0700https://chtsai0105.github.io/media/icon_hu_6ea0838c0c3bf85b.pnghttps://chtsai0105.github.io/tags/orthology/https://chtsai0105.github.io/projects/orthosynassign/Wed, 12 Aug 2026 22:48:23 -0700https://chtsai0105.github.io/projects/orthosynassign/<p><strong> </strong> is a high-performance, open-source bioinformatics tool engineered to refine coarse, over-aggregated orthogroups into high-resolution, true orthologs by leveraging local syntenic context.</p> <p>While sequence similarity-based clustering methods (such as OrthoFinder) excel at high-throughput orthology inference, they often produce broad, many-to-many clusters contaminated with confounding paralogs. <strong> </strong> acts as a drop-in downstream refinement engine that evaluates conserved gene order along chromosomal neighborhoods to untangle complex gene families, segregate paralogous copies, and isolate strict single-copy orthologs for phylogenomics.</p> <hr> <h3 id="core-architecture--key-innovations">Core Architecture &amp; Key Innovations</h3> <ul> <li><strong>Python + Rust Hybrid Engine:</strong> Combines an intuitive, object-oriented Python interface with a lightning-fast calculation core written in Rust (via <code>PyO3</code>), bypassing Python’s Global Interpreter Lock (GIL) for true multi-core parallel execution.</li> </ul> <p> <figure > <div class="flex justify-center "> <div class="w-full" ><img alt="benchmark" src="https://chtsai0105.github.io/projects/orthosynassign/benchmark_multithreads.svg" loading="lazy" data-zoomable /></div> </div></figure> </p> <ul> <li><strong>Tandem Repeat Pre-Collapsing:</strong> Explicitly consolidates adjacent, duplicated genes into single syntenic units prior to sliding-window scans, preventing artificial window expansion and misaligned orthology.</li> <li><strong>Graph-Based Disjoint Set Union (DSU) Clustering:</strong> Utilizes graph-modeled pairwise synteny and DSU clustering with path compression for rapid, memory-efficient multi-species orthogroup resolution.</li> <li><strong>Built-in Visualization &amp; Utility:</strong> Includes a GFF-to-BED conversion utility (<code>gff2bed.py</code>) and a companion visualization script (<code>orthosynassign-vis</code>) to render local genomic neighborhoods and synteny blocks.</li> </ul> <p> <figure > <div class="flex justify-center "> <div class="w-full" ><img alt="vis" src="https://chtsai0105.github.io/projects/orthosynassign/OG0000012_combined.svg" loading="lazy" data-zoomable /></div> </div></figure> </p>