hypothetical-asr-fitch

hypothetical-asr-fitch is a skill for Claude Code, Codex from agentlas-ai/agentlas-desktop. It costs 39 tokens per session (272 once invoked), scanned A, original, Apache-2.0.

An exploratory method for listing possible DNA states at one internal node of a rooted, branching evolutionary tree. Fitch parsimony chooses states using the fewest changes and reports ambiguity rather than probabilities.

In plain words
What is it for?
It helps inspect hypothetical ancestral state sets from an observed DNA alignment before more rigorous evolutionary analysis.
Why use it?
It prevents an ambiguous reconstruction from being presented as a confirmed ancestral genome, extinct species, or biological result.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

Good fit It helps inspect hypothetical ancestral state sets from an observed DNA alignment before more rigorous evolutionary analysis.

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Install with agentmods
npx agentmods add skills/agentlas-ai/agentlas-desktop/hypothetical-asr-fitch
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 agentlas-ai/agentlas-desktop --skill hypothetical-asr-fitch
Clone the repo
git clone --depth 1 https://github.com/agentlas-ai/agentlas-desktop

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.

agentmods badge for hypothetical-asr-fitch

README.md
[![agentmods](https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/hypothetical-asr-fitch/github.svg)](https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/hypothetical-asr-fitch)
Your own site
<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/hypothetical-asr-fitch"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/hypothetical-asr-fitch/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.

agentmods 80×15 button for hypothetical-asr-fitch

Your own site · 80×15
<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/hypothetical-asr-fitch"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/hypothetical-asr-fitch.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 39 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 272 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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00039 $0.00272
Opus 5.5 $0.00016 $0.00109
Sonnet 5.5 $0.00008 $0.00054
Haiku 4.5 $0.00004 $0.00027

Measured 1mo ago against content hash 738db6bd516c, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

hypothetical-asr-fitch 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 1mo ago.

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.

plugins/agentlas-comparative-genomics/skills/hypothetical-asr-fitch/SKILL.md · 19 lines

What it actually says

Hypothetical Fitch ASR

Use this workflow only as an exploratory inspection of ambiguity sets.

  1. Require a sealed comparative-genomics parent ResearchRun with sequenceType: cdna.
  2. Re-read and hash-verify the exact parent assessment output from CAS.
  3. Require a rooted strictly bifurcating tree whose leaves exactly match the observed extant DNA alignment.
  4. Require the caller to select a non-root internal node. Do not silently choose a named ancestor or terminal species.
  5. Run deterministic Fitch parsimony and preserve all ambiguous state sets. Do not add posterior probability, likelihood, or confidence fields.
  6. Label the result and every reconstructed site hypothetical.
  7. Preserve and open the exact ResearchRun-bound site table and ambiguity-Figure artifact in the Comparative Genomics Lab before interpreting it.
  8. Do not call the display sequence a recovered ancestral sequence, extinct genome, chromosome, phenotype, viable embryo, or hatching result.
  9. For publication-grade ASR, stop and require independent alignment, substitution-model, topology, taxon-sampling, probabilistic reconstruction, and experimental validation.
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.

  1. 1mo ago First seen · 19 lines · 39 tokens per session scan A 738db6bd516c

Subscribe to this mod's changes

hypothetical-asr-fitch is a skill published in the GitHub repository agentlas-ai/agentlas-desktop (6 stars, last pushed yesterday), licensed Apache-2.0. It adds 39 tokens to every session and 272 once invoked, about $0.0002 per session on Opus 5.5. 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 2026-09-04.

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