MolecularClockSimulation
A Python toolkit for simulating sequence evolution and exploring molecular clock algorithms
What XERJ indexed
Snapshot
The whole repository at commit 19a9e5a325. It is the newest commit on main.
Selected work
Licence
The repository
LICENSE file checked at the pinned commit; the author agreed to inclusion.
The XERJ corpus
The owner added it on hub.xerj.org after signing in with GitHub, on 2026-10-31. Same terms as the repository. Answers name the repo, the commit and the file:line.
selected for the XERJ Corpus Hublicence clearedsuggested use: adapt with attribution
bioinformaticscomputational-biologyeducationalevolutionmolecular-clockphylogeneticspythonscientific-computing
Example questions
- How does MolecularClockSimulation implement bioinformatics?
- Show the computational-biology code in MolecularClockSimulation.
Inside the indexed corpus
- 290 files, 4.3 MB in total, about 15.3 KB per file.
- Languages by size: Python 98.4%, Shell 1.3%, Dockerfile 0.3%.
- On GitHub since 2026-07-06, last push 2026-07-15, 102 commits on main.
Licence on GitHub and in the corpus
GitHub reported MIT for davewalker5/MolecularClockSimulation on 2026-10-31, and the LICENSE file at commit 19a9e5a325 was reviewed as MIT. They match, so answers from this corpus carry the same terms as the live repository.
Contributors
Dave Walker (@davewalker5) has 14 selected repositories on the hub.
Their other repository pages: davewalker5/ADS-B-BaseStationReader, davewalker5/FossilTracker, davewalker5/ChromatophoreSimulator, davewalker5/OctopusController, davewalker5/FishTrack, davewalker5/LogSpiral.
Using XERJ with MolecularClockSimulation
- Index a reference library for a coding agent
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The prompt
Paste it into your AI agent. It clones davewalker5/MolecularClockSimulation at the pinned commit and indexes it on your machine.
Search the GitHub repository davewalker5/MolecularClockSimulation with XERJ (https://hub.xerj.org/corpus/davewalker5--molecularclocksimulation). Run these in a shell, in order, and check each result before the next: 1. xerj --help (success: it prints usage). If xerj is missing: curl -fsSL https://xerj.org/get | sh 2. git clone https://github.com/davewalker5/MolecularClockSimulation MolecularClockSimulation && git -C MolecularClockSimulation checkout 19a9e5a3254217d3694cd66d6e9f2a7c0e712d1a 3. Start a local node and leave it running: xerj --insecure --data-dir ./xerj-data 4. xerj autoindex ./MolecularClockSimulation --url http://127.0.0.1:9200 --prefix molecularclocksimulation --progress plain 5. xerj autoindex map --url http://127.0.0.1:9200 Then answer my question from the indexed files and cite the ax_path of every hit. Query syntax: https://xerj.org/llms.txt Licence: MIT. Keep the copyright notice and credit the authors.
Related
Dave WalkerHealth and clinical reference corporascispacyplan-and-actsyntheaMuteJester/GenAIRRscikit-bio/scikit-bioAtharvaTilewale/boltz2-notebook
Stats: GitHub API, fetched 2026-10-31. Snapshot: the git tree at the pinned commit. Selected work and consent: the XERJ registry.