HogProf

• HogProf is an extensible and tunable approach to phylogenetic profiling using orthology data. It is powered by minhash based datastructures and computationally efficient.

• Still under major development and may change.

Installation

To install My Project, run the following command:

Using pip

Or from github .. code-block:: bash $ git clone https://github.com/DessimozLab/HogProf.git $ pip install -r pipreqs.txt .

Quickstart

To use the library we need an OMA instance’s HDF5 file containing HOG info and some accesory files.

Let’s create a directory for the phylogenetic rpfiling database were going to make.

Ok. We’re ready! Now let’s compile a database containing all HOGs and our desired taxonomic levels using default settings. Launch the lshbuilder. dbtypes available on the command line are : all , plants , archaea, bacteria , eukarya , protists , fungi , metazoa and vertebrates. These will use the NCBI taxonomy as a tree to annotate events in different gene family’s histories.

This should build a taxonomic tree for the genomes contained in the release and then calculate enhanced phylogenies for all HOGs in OMA. Once the database is completed it can be interogated using a profiler object. Construction and usage of this object should be done using a python script or notebook.

Troubleshooting

If you encounter any issues while using My Project, please file a bug report on our GitHub repository: https://github.com/user/repo/issues

Credits

My Project was created by John Doe.