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  • v1.0-paper

    afb705b6 · Including final analysis up until June 13 2026 ·
    Release: RECOSIM v1.0, the version described in the dengue paper 
    RECOSIM as described in de Paula Oliveira et al.

Version of RECOSIM described in:

  de Paula Oliveira, H., Jacob Machado, D., Prieto-Oliveira, P., and
  Ocana, K. Evidence for recombination in dengue virus genomes.
  Submitted, 2026.

Detection clusters YBYRA-categorized character-state transformations with
DBSCAN, in three strategies (regularClusters, expandingClusters and
expandingNotDeleting) under the parameters epsilon, min_samples,
overlap_threshold and identity_threshold. The paper reports
recosim_regularClusters.py with o=30, i=0.95, e=30, m=3.

The detection scripts are in 4_detect_recombinations/, with the benchmark
inputs and results beside them. Supplementary materials for the paper:
https://doi.org/10.5281/zenodo.20059036

Later commits on main replace this with a redesigned detector. This tag is
the code the paper describes.