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Multiple sequence alignment tool with high accuracy and high throughput — one of the best-performing multiple alignment programs.
Use with AI
Install the MCP server or CLI to instantly fetch MUSCLE documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/muscle
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2 shared topics • 1 shared operation
ClonalFrameML detects recombination (horizontal gene transfer) in bacterial whole-genome alignments using maximum likelihood inference. It takes a Newick phylogenetic tree and FASTA/XMFA alignment, th
2 shared topics • 1 shared operation
GTDB-Tk — toolkit for objective taxonomic classification of bacterial and archaeal genomes using the Genome Taxonomy Database (GTDB). Assigns taxonomy based on placement in reference trees inferred fr
2 shared topics • 1 shared operation
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