This repository contains test input files and experimental datasets for the PhyloProfile tool.

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 via the PhyloProfileData package (source code can be found here).

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.

The otherExpTestData folder contains two additional experimental datasets.
These can be downloaded and manually provided to PhyloProfile for testing or analysis.

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.

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