rna_small_parsimony

Some code to experiment around the different notions of distances to solve the small parsimony problem on RNA structures.

Steps to reproduce results

pip install .

To install the package rnadist, which includes useful routines.

Then, with the Rfam.seed file placed in the experiments/rf_small_parsimony/resources folder, execute in that same folder

python3 extract_seed_alignments.py

Also, retrieve from RFAM the ``tree files'' zip and extract it into the tree_files subfolder.

Finally, in the experiments/rf_small_parsimony folder, execute

snakemake -c[number of cores]

To produce all the data (might take some time).