Skills

A skill is a package of structured files that teaches an AI coding agent how to work with a specific tool or framework. The skill below was generated by Great Docs from this project’s documentation. Install it in your agent and it will be able to run commands, edit configuration, write content, and troubleshoot problems without step-by-step guidance from you.

Any agent — install with npx:

npx skills add https://datasnakes.github.io/OrthoEvolution/

Codex / OpenCode

Tell the agent:
Fetch the skill file at https://datasnakes.github.io/OrthoEvolution/skill.md and follow the instructions.

Manual — download the skill file:

curl -O https://datasnakes.github.io/OrthoEvolution/skill.md

Or browse the SKILL.md file.

SKILL.md

---
name: orthoevol
description: >
  This package aids in the analysis of orthologous genes. Use when writing Python code that uses the OrthoEvol package.
license: MIT
compatibility: Requires Python >=3.11,<3.15.
---

# OrthoEvolution

This package aids in the analysis of orthologous genes.

## Installation

```bash
pip install OrthoEvol
```

## API overview

### Ortholog discovery

Infer orthologs and summarize comparative-genetics results.

- `Orthologs.Blast.BaseComparativeGenetics`
- `Orthologs.Blast.ComparativeGenetics`
- `Orthologs.Blast.BaseBlastN`
- `Orthologs.Blast.OrthoBlastN`

### Sequence retrieval

Retrieve and organize GenBank records and NCBI datasets.

- `Orthologs.GenBank.GenBank`
- `Tools.ftp.BaseFTPClient`
- `Tools.ftp.NcbiFTPClient`
- `Tools.mygene.MyGene`

### Alignment and phylogenetics

Prepare alignments and run supported phylogenetic programs.

- `Orthologs.Align.ClustalO`
- `Orthologs.Align.Guidance2Commandline`
- `Orthologs.Align.Pal2NalCommandline`
- `Orthologs.Align.MultipleSequenceAlignment`
- `Orthologs.Phylogenetics.RelaxPhylip`
- `Orthologs.Phylogenetics.ETE3PAML`
- `Orthologs.Phylogenetics.PhyML`
- `Orthologs.Phylogenetics.Phylip`
- `Orthologs.Phylogenetics.IQTreeCommandline`
- `Orthologs.Phylogenetics.FilteredTree`
- `Orthologs.Phylogenetics.TreeViz`
- `Orthologs.Phylogenetics.PAML.CodemlRun`

### Project and data management

Create project layouts and coordinate data and database workflows.

- `Manager.management.Management`
- `Manager.management.RepoManagement`
- `Manager.management.UserManagement`
- `Manager.management.WebsiteManagement`
- `Manager.management.ProjectManagement`
- `Manager.data_management.DataMana`
- `Manager.database_management.BaseDatabaseManagement`
- `Manager.database_management.DatabaseManagement`
- `Manager.database_dispatcher.DatabaseDispatcher`
- `Manager.biosql.biosql.BaseBioSQL`
- `Manager.biosql.biosql.SQLiteBioSQL`
- `Manager.biosql.biosql.MySQLBioSQL`

### Execution and supporting tools

Run local, PBS, Slurm, logging, and transfer helpers.

- `Tools.pbs.BaseQsub`
- `Tools.pbs.Qsub`
- `Tools.pbs.BaseQstat`
- `Tools.pbs.Qstat`
- `Tools.pbs.MultiQstat`
- `Tools.pbs.TargetJobKeyError`
- `Tools.slurm.SlurmClient`
- `Tools.slurm.SlurmJob`
- `Tools.slurm.SlurmCommandNotFoundError`
- `Tools.parallel.Multiprocess`
- `Tools.logit.LogIt`
- `Tools.pybasher.PyBasher`
- `Tools.send2server.S2S`
- `Tools.slackify.Slackify`

### Templates and utilities

Create project templates and use shared package utilities.

- `Cookies.Oven`
- `Cookies.CookBook`
- `resources.package_resource_path`
- `utilities.DuplicateAnalysis`
- `utilities.BlastUtils`
- `utilities.GenbankUtils`
- `utilities.OrthologUtils`
- `utilities.ManagerUtils`
- `utilities.CookieUtils`
- `utilities.PackageVersion`
- `utilities.FunctionRepeater`
- `utilities.FullUtilities`
- `OrthoEvolWarning`: This is the OrthoEvol main warning class
- `OrthoEvolDevelopmentWarning`: This is the OrthoEvol developmental code warning subclass
- `OrthoEvolDeprecationWarning`: This is the Deprecation Warning subclass

## Resources

- [Full documentation](https://datasnakes.github.io/OrthoEvolution/)
- [llms.txt](llms.txt) — Indexed API reference for LLMs
- [llms-full.txt](llms-full.txt) — Comprehensive documentation for LLMs
- [Source code](https://github.com/datasnakes/OrthoEvolution)