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Use when working with UShER (Ultrafast Sample placement on Existing tRees) for phylogenetic placement of new samples onto existing mutation-annotated trees. Places sequences via maximum parsimony on l
Use with AI
Install the MCP server or CLI to instantly fetch UShER documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/usher
docker pull biocontainers/usher:0.6.6BEAST2 — Bayesian Evolutionary Analysis by Sampling Trees. Cross-platform Java application for Bayesian phylogenetic inference using MCMC sampling. Use when estimating time-calibrated phylogenies, rel
1 shared topic • 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
1 shared topic • 1 shared operation
Gubbins — rapid phylogenetic analysis of recombinant bacterial whole genome sequences. Iteratively detects recombination hotspots with elevated SNP density while constructing clonal frame phylogenies.
1 shared topic • 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
1 shared topic • 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
1 shared topic • 1 shared operation