https://github.com/bionf/phyloprofile-data

Data files for PhyloProfile tool
https://github.com/bionf/phyloprofile-data

Last synced: 4 months ago
JSON representation

Data files for PhyloProfile tool

• Host: GitHub
• URL: https://github.com/bionf/phyloprofile-data
• Owner: BIONF
• License: mit
• Created: 2018-01-30T14:11:55.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2025-10-20T08:06:13.000Z (8 months ago)
• Last Synced: 2025-10-20T10:10:13.279Z (8 months ago)
• Size: 348 MB
• Stars: 1
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
# PhyloProfile Test and Experimental Data

This repository contains **test input files** and **experimental datasets** for the [**PhyloProfile**](https://bioconductor.org/packages/PhyloProfile) tool.

---

## Demo Datasets

The archives **`ampk-tor.zip`** and **`arthropoda.zip`** include data for two demo datasets used by PhyloProfile.  

These datasets are also available through [**Bioconductor ExperimentHub**](https://bioconductor.org/packages/release/bioc/html/ExperimentHub.html) via the **PhyloProfileData** package (source code can be found [here](https://github.com/BIONF/PhyloProfileData)).

They are used to demonstrate how to run PhyloProfile and analyze its results.  

Briefly, it contains phylogenetic profiles, FASTA sequences, and domain annotations for two experimental datasets:

- **AMPK–TOR pathway dataset:**  

  147 human proteins involved in the AMPK–TOR pathway across 83 species.

- **Arthropoda dataset:**  

  1,011 BUSCO arthropoda ortholog groups across 88 species spanning the three domains of life.

---

## Other Experimental Data

The **`otherExpTestData`** folder contains two additional experimental datasets.  

These can be downloaded and manually provided to PhyloProfile for testing or analysis.

---

## Demo Input Files

The **`demoInput`** folder includes several example input files in various formats.  

To learn how to correctly format input data for PhyloProfile, please refer to our [**Wiki page**](https://github.com/BIONF/PhyloProfile/wiki/Input-Data).

---

## References

Ngoc-Vinh Tran, Bastian Greshake Tzovaras, Ingo Ebersberger, PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages 3041–3043, https://doi.org/10.1093/bioinformatics/bty225