Welcome to PhyloHiC’s documentation!

PhyloHiC is a set of scripts that allows the computation of distances between genomes based on shared genomic regions and genomic contact data. Currently, we use orthologous genes as shared regions and Hi-C data as contacts information. Thus, you must already have these data.

License

The source code is available here and is licensed under the CeCILL V2.1 since it was written when I was working in a CNRS laboratory. The CeCILL license is close to the GNU GPL and compatible with it. The full text for the license is available in the LICENSE file in the repository.

Citing

PhyloHiC has been written during my PhD thesis work, and is described in the third chapter of my thesis (in French). Moreover, the results presented there come from the pipeline documented here. Thus, if you use this pipeline, please cite my thesis:

Sylvain Pulicani.
Lien entre les réarrangements chromosomiques et la structure de la chromatine chez la Drosophile.
Autre [cs.OH]. Université Montpellier, 2018. Français.
NNT: 2018MONTS105
HAL: tel-02161932

Please note that a scientific publication is coming.

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This documentation is divided in three sections:

• 1. Introduction and General Process
  • 1.1. Main Idea
  • 1.2. General Process
  • 1.3. Parameters
• 2. A few concepts to define
  • 2.1. Genes Adjacency
  • 2.2. Values selection mode
  • 2.3. Randomization
• 3. Preparing Data and Running an Analysis
  • 3.1. Prepare the data
  • 3.2. Running the pipeline
  • 3.3. Results
• 4. Scripts and API documentation
  • 4.1. Scripts
  • 4.2. API
• 5. File Formats
  • 5.1. Experiment Configuration file
  • 5.2. Hi-C dataset format
  • 5.3. Orthologous Genes File
  • 5.4. Pairs File
  • 5.5. Basic Statistics Intermediate File
  • 5.6. Values File