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ETE Toolkit — Python library for phylogenetic tree exploration, manipulation, and analysis. Provides tree parsing (Newick, Nexus), database connectivity (NCBI Taxonomy, GTDB), interactive visualizatio
Use with AI
Install the MCP server or CLI to instantly fetch ETE Toolkit documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/ete-toolkit
Anvi'o — integrated analysis and visualization platform for 'omics data. Supports metagenomics (MAG binning, refinement, read recruitment), pangenomics (gene cluster analysis, ANI computation), phylog
2 shared topics • 1 shared operation
ggtree — R/Bioconductor package for phylogenetic tree visualization and annotation using ggplot2 grammar. Supports Newick, Nexus, NHX, Jplace, and BEAST tree formats. Enables layer-based annotation wi
2 shared topics • 1 shared operation
Harvest Tools — core genome phylogenomics suite for rapid whole-genome alignment, SNP extraction, and phylogenetic tree inference from closely related microbial genomes. Parsnp performs MUMmer-based c
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
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