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Roary — rapid large-scale prokaryotic pan genome analysis. Calculates the pan genome from annotated assemblies (GFF3 from Prokka/Bakta), producing core and accessory gene clusters, gene presence/absen
Use with AI
Install the MCP server or CLI to instantly fetch Roary documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/roary
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2 shared topics • 2 shared operations
ParSNP — rapid core-genome alignment and SNP detection for closely related microbial genomes (bacteria, archaea). Part of the HARVEST suite alongside HarvestTools and Gingr. Aligns hundreds of whole-g
2 shared topics • 2 shared operations
Gubbins — rapid phylogenetic analysis of recombinant bacterial whole genome sequences. Iteratively detects recombination hotspots with elevated SNP density while constructing clonal frame phylogenies.
3 shared topics
OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se
2 shared topics • 1 shared operation
TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) is a Java-based software package for genome-wide association studies (GWAS), population genetics, and linkage disequilibrium analysis. Su
2 shared topics • 1 shared operation