FastTree — approximately maximum-likelihood phylogenetic tree inference from nucleotide or protein sequence alignments. Infers large phylogenies (up to 1M sequences) 100-1000x faster than RAxML or Phy
Use with AI
Install the MCP server or CLI to instantly fetch FastTree documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/fasttree
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
2 shared topics • 2 shared operations
PAML — Phylogenetic Analysis by Maximum Likelihood. Suite of programs for phylogenetic analysis of DNA and protein sequences using maximum likelihood. Includes codeml (codon/amino acid models, dN/dS s
2 shared topics • 2 shared operations
PhyloBayes — Bayesian MCMC phylogenetic inference software using infinite mixture models (CAT, CAT-GTR) of amino acid or nucleotide substitution. Runs parallel MCMC chains, assesses convergence with b
2 shared topics • 2 shared operations
Deep learning system for protein structure prediction from amino acid sequence with atomic accuracy — revolutionized structural biology.
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