Published January 11, 2023 | Version v4
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Role for gene conversion in the evolution of cell-surface antigens of the malaria parasite Plasmodium falciparum

  • 1. EMBL-EBI
  • 2. Genomics England


Documentation, figures, software freeze and singularity container supporting the following research article:

The file starting with  `paper_pfalciparum_DBs` is an archive of the github repository

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 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 `` 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



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