Data & ReproStatistics & Data AnalysisFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-epidemiological-genomics-phylodynamics

Maintainer FreedomIntelligence · Last updated April 1, 2026

Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times, molecular clock rates, and ancestral states. Use when dating outbreak origins, estimating transmission rates, or building time-calibrated trees.

OpenClawNanoClawAnalysisReproductionbio-epidemiological-genomics-phylodynamics🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epidemiological & causal genomicsconstruct

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-epidemiological-genomics-phylodynamics

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Python: treetime.TreeTime() for maximum likelihood time-scaled trees.
CLI: treetime --tree tree.nwk --aln aln.fasta --dates dates.tsv.
Build a time-scaled tree for my outbreak" → Estimate divergence times and molecular clock rates from dated sequences to reconstruct outbreak timing and evolutionary dynamics. Python: treetime.TreeTime() for maximum likelihood time-scaled trees CLI: treetime --tree tree.nwk --aln aln.fasta --dates dates.tsv.
tree = Phylo.read('tree.nwk', 'newick').

Source Doc

Excerpt From SKILL.md

TreeTime Basic Usage

from treetime import TreeTime
from Bio import Phylo

## Date formats: 2020.5, 2020-06-15, numeric (decimal year)

tt = TreeTime(
    tree=tree,
    aln='alignment.fasta',
    dates='dates.tsv',
    gtr='JC69'  # Nucleotide model: JC69, HKY85, GTR
)

## Run molecular clock analysis

tt.run(
    root='best',           # Root optimization: 'best', 'least-squares', or clade name
    Tc='skyline',          # Coalescent prior: None, 'skyline', 'opt', or numeric
    time_marginal='assign_ml'  # Date estimation method
)

Use cases

Use when dating outbreak origins, estimating transmission rates, or building time-calibrated trees.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

epidemiological-genomics/transmission-inference - Infer who-infected-whom
phylogenetics/modern-tree-inference - Build input phylogeny
epidemiological-genomics/variant-surveillance - Track lineage dynamics

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