This project contains the codes for replicating the analyses of "Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses", R Maestri, B Perez-Lamarque, A Zhukova, H Morlon, eLife, 2024.
List of the files:
- script_covid.sh: bash script for reconstructing the phylogenetic trees (PhyloBayes, BEAST) and doing cophylogenetic analyses (ALE, eMPRess).
- script_covid.R: R script for analyzing the results of cophylogenetic analyses, generating simulations and making the figures.
- functions_cospeciation_covid.R and llpruning.c: functions to perform the simulations of codiversification.
Contact: Benoît Perez-Lamarque (benoit.pere.lamarque@gmail.com) and Renan Maestri (renanmaestri@gmail.com)
Citation: Renan Maestri, Benoît Perez-Lamarque, Anna Zhukova, Hélène Morlon, 2024, Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses, eLife, 13:RP91745
