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Detect syntenic gene blocks and structural rearrangements between genomes using MCScanX, JCVI, GENESPACE, SyRI, AnchorWave and related tools; guidance on pipeli
Provides a practical, publication-oriented workflow for detecting syntenic blocks and structural rearrangements between genomes. The skill explains which tools to use (MCScanX/JCVI for collinearity, GENESPACE for plant multi-genome orthology-anchored synteny, SyRI/plotsr for structural variants, AnchorWave for WGD-aware alignment), concrete command examples, and post-processing checks (repeat-masking, BUSCO, Ks dating). It includes per-tool failure modes and quantitative thresholds for reliable results.
Use this skill when you need to compare genome architectures across species, identify inversions/translocations/duplications, build riparian/pan-gene visualizations for plants, or run synteny-aware ortholog inference in polyploid lineages. It applies to publication analyses, QC of assemblies before comparative work, and generating figures (dotplots, riparian plots, SV maps).
This skill is documentation-focused and tool-agnostic; it maps to Linux/conda environments invoking CLI tools and Python/R pipelines (suitable for agents that can run shell/python/R commands or invoke MCP tools that wrap these bioinformatics tools).
This skill has not been reviewed by our automated audit pipeline yet.
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