.. PhyloHiC documentation master file, created by sphinx-quickstart on Tue Jun 5 11:14:13 2018. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. 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. ------------------------------------------------------------------------------- This documentation is divided in three sections: .. toctree:: :numbered: :maxdepth: 2 intro definitions analysis scripts_and_api file_formats .. _my thesis: https://tel.archives-ouvertes.fr/tel-02161932 .. _here: https://gite.lirmm.fr/pulicani/phyloHiC .. _CNRS: https://www.cnrs.fr/en .. _LICENSE file in the repository: https://gite.lirmm.fr/pulicani/phyloHiC/blob/master/LICENSE