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Script to pre-process GWAS inputs

Import Matlab *.mat files as sequences in Icy

SMARTdenovo assembly tool wrapped into a singularity for HPC cluster executions

A patched version of the Jama library. Internal structures accessors and package name added. The original version can be found here : http://math.nist.gov/javanumerics/jama/

Extracting CDS from contig sequences

This will contain the minimal necessary codes to reproduce the image analysis (BF and IF) from the preprint https://arxiv.org/abs/2303.17522

Data and code of the article Rasoamalala et al. "Unraveling the role of rat and flea population dynamics on the seasonality of plague epidemics in Madagascar", Proceedings of the National Academy of Sciences (2025).