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Use when predicting variant pathogenicity with EVE (Evolutionary model of Variant Effect) — an unsupervised deep generative model from the Marks Lab (OATML/Harvard) that scores missense variants using
Use with AI
Install the MCP server or CLI to instantly fetch EVE documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/eve
BEAST2 — 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 • 2 shared operations
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 • 2 shared operations
PhyML — maximum likelihood phylogenetic inference from nucleotide and amino acid sequence alignments. Supports GTR, HKY, K80, JC, and 15+ DNA/protein substitution models, gamma rate heterogeneity (+G)
1 shared topic • 2 shared operations
RAxML-NG — maximum likelihood phylogenetic tree inference using iterative SPR moves with libpll likelihood computation. Supports DNA, protein, binary, and multi-state data with partitioned analyses, n
1 shared topic • 2 shared operations
TreeTime — maximum likelihood molecular clock inference, ancestral sequence reconstruction, and phylodynamic analysis from time-stamped phylogenies. Infers timetrees by iteratively optimizing ancestra
1 shared topic • 2 shared operations