Phylogeny-Partners

Two states models

Instalation

You may need to install the cython, networkx, numpy, scipy package:

pip install cython, networkx, numpy, scipy

and do in the folder two_states :

cd 2_states/code_two_states
cythonize -i generation_sequences.pyx
cythonize -i mutual_info.pyx

To use the last part of the jupyter notebook figures.ipynb, you should install bmDCA :

https://github.com/ranganathanlab/bmDCA

The code works on linux and Mac. (It is possible to adapt it for windows, you need to change the drand48() or random() function by one available in windows distribution)

Utilisation

You can open figures.ipynb and different_graph.ipynb to see all figures generated with the simple model.

Twenty one states models

Installation

The code present in Code_for_cluster was present in the EPFL cluster. It is helpful to generate data and to infer contact and partners. The model has been inferred with bmDCA on the cluster and arDCA on my personal computer. If you want to reproduce the data, I advise you to copy the folder Code_for_cluster and to do :

cd 21_states/Code_for_cluster/cython_code/
cythonize -i generation_sequence.pyx
cythonize -i generation_sequence_arDCA.pyx
cythonize -i analyse_sequence.pyx 

Generation of data

And after, you can generate MSA (data set of aligned sequences) :

sbatch generation_sequence_bmDCA.run
sbatch generation_sequence_arDCA.run

If you are not on a cluster and cannot use the function sbatch, you can replace sbatch by bash.

Inference

When these three programmes are completed, you can infer the contact with :

sbatch inference_contact.run

And for the partners :

sbatch inference_partners_generated_data.py

If you want to see the plot from the inference, you can run the jupyter notebook inside the folder 21_states.

2 states with sampling on a inferred model

Installation

See 2_states_generation_inference/README.md

Figures

See generating_data_fasta.ipynb