Role for gene conversion in the evolution of cell-surface antigens of the malaria parasite Plasmodium falciparum

Documentation, figures, software freeze and singularity container supporting the following research article: https://doi.org/10.1371/journal.pbio.3002507

The file starting with  `paper_pfalciparum_DBs` is an archive of the github repository https://github.com/iqbal-lab-org/paper_pfalciparum_DBs

Files for reproducibility:

• output_analysed_sequences.tar.gz contains all the output sequences (unaligned FASTAs and multiple-sequence alignments) analysed in the paper. Notably, the one used to build the clustering tree is 'analysis/outputs/analysed_sequences/gramtools/DBs/protein/DBs_full_with_pf_and_laverania_assemblies.msa'/
• input_analysed_sequences_for_plasmo_paralogs.tar.gz contains all the input sequences that were used to produce the output sequences just above
• Files in `input_tsvs.tar.gz` are input data tables, located under `analysis/input_data` on the github repository
• FIle `singu.sif` is a singularity container containing all the software used in support of the article, and should be placed at `reproducibility/container/built/singu.sif` in the github repository in order to rerun the analysis workflows and replicate the results (see README.md on the github repository).
• Files in `output_data_for_figures.tar.gz` contain the raw data needed to plot each of the figures (main and supplementary) of the paper. See the `README.md` in there for instructions on how.

Figures and documentation:

• File `figures_recombination_breakpoints_all.pdf` contains all mosaic alignments, and is also available at `/plasmo_paralogs/docs/latex_recomb_images/doc.pdf` on the github repository
• Files starting with `docs` contain useful information, and are available in the `docs` folders on the github repository