Use it to reconstruct ancestral DNA or protein sequences, map discrete traits onto a tree, and estimate ancestral continuous measurements.

It lets researchers study evolutionary history when the ancestral organism or sequence cannot be observed directly.

bio-comparative-genomics-ancestral-reconstruction

Q: What is bio-comparative-genomics-ancestral-reconstruction?

A bioinformatics workflow for estimating what genes, sequences, or traits may have looked like in ancestral species. It uses a family tree of species or genes and models how states change along its branches.

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add GPTomics/bioSkills --skill ancestral-reconstruction

Clone the repo

git clone --depth 1 https://github.com/GPTomics/bioSkills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gptomics/bioskills/ancestral-reconstruction/github.svg)](https://agentmods.dev/skills/gptomics/bioskills/ancestral-reconstruction)

Your own site

<a href="https://agentmods.dev/skills/gptomics/bioskills/ancestral-reconstruction"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/ancestral-reconstruction/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/gptomics/bioskills/ancestral-reconstruction"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/ancestral-reconstruction.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 149 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 9,696 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00149	$0.09696
Opus 5	$0.00075	$0.04848
Sonnet 5	$0.00030	$0.01939
Haiku 4.5	$0.00015	$0.00970

Measured 7d ago against content hash b6b72971d3b5, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

bio-comparative-genomics-ancestral-reconstruction scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (examples/ancestral_reconstruction.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

bio-comparative-genomics-ancestral-reconstruction — 97% identical, 12 lines differ

comparative-genomics/ancestral-reconstruction/SKILL.md · 476 lines

How it starts

The opening of the file, as written. The whole thing — 476 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Version Compatibility

Reference examples tested with: PAML 4.10.7+, IQ-TREE 2.3.6+, GRASP 2024+ (web/CLI), FastML 3.11+, RevBayes 1.2.4+, BayesTraits V4.1+, R 4.4+, ape 5.8+, phytools 2.3+, corHMM 2.9+, geiger 2.0.11+, phangorn 2.12+, RERconverge 0.3.0+, BioPython 1.84+.

Before using code patterns, verify installed versions match. If versions differ:

R: packageVersion('corHMM') then ?ancRECON, ?make.simmap, ?ace
CLI: codeml (no --version; check paml -h or examine Phylip.tre example), iqtree2 --version, revbayes --version
Python: pip show biopython; check Bio.Phylo.PAML.codeml API

If code throws AttributeError, ImportError, missing slot errors on R S4 objects, or PAML mlc parsing failures, introspect the installed package (? in R, help() in Python) and adapt the example rather than retrying. PAML output formats are stable across 4.9 -> 4.10; IQ-TREE's --ancestral flag replaced -asr in v2.0+.

Ancestral State Reconstruction

"What did this gene / trait / genome look like at an internal node?" -> Choose the reconstruction framework that matches the data class (sequence / discrete trait / continuous trait / gene content) and the inference question (point estimate vs full posterior; marginal vs joint vs scaled-conditional). The single most common mistake is reconstructing under a site-independent or trait-stationary model when the underlying biology demands a hidden-rate or epistatic model -- the resulting "ancestor" is mathematically optimal under the wrong model and is silently wrong (Beaulieu & O'Meara 2016 Syst Biol 65:583; Boyko & Beaulieu 2021 MEE 12:468).

Sequence ASR (protein resurrection): PAML codeml RateAncestor=1; IQ-TREE2 --ancestral; GRASP (graph-based, handles indels); FastML (Bayesian)
Discrete traits: R ape::ace(type='discrete'); corHMM::corHMM() (rate categories); phytools::make.simmap() stochastic mapping; BayesTraits MultiState/Discrete
Continuous traits: phytools::fastAnc(); phytools::contMap(); geiger::fitContinuous(model='BM'|'OU'|'EB'); RPANDA fit_t_env()
Ancestral gene content (presence/absence): ape::ace(type='discrete', model='ARD'); Dollo parsimony in phangorn; ALE/GeneRax for full DTL (see [[gene-tree-species-tree-reconciliation]])

Read the full file on GitHub · 476 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

7d ago First seen · 476 lines · 149 tokens per session scan A b6b72971d3b5

Subscribe to this mod's changes

bio-comparative-genomics-ancestral-reconstruction is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 149 tokens to every session and 9,696 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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