Probabilistic programme to calculate speciation and extinction rate using a constant rate birth death model on a given phylogenetic tree
To start the calculation of the parameters with a quick analytical approach (assumes incomplete sampling, rho is encoded in the analysis file):
yarn start
To start the calculate of the parameters with a more exhaustive simulation approach:
yarn start-sim
Show a rough histogram of the samples (requires global python3 and bashplotlib)
yarn distribution
Probabilistic programming: a powerful new approach to statistical phylogenetics Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström, Nicolas Lartillot, Daniel Lundén, Lawrence Murray, Thomas B. Schön, David Broman
doi: https://doi.org/10.1101/2020.06.16.154443
Transitions between biomes are common and directional in Bombacoideae (Malvaceae) Zizka, Alexander; Carvalho-Sobrinho, Jefferson; Pennington, Toby R.; Queiroz, Luciano; Alcantara, Suzana; Baum, David; Bacon, Christine D.; Antonelli, Alexandre
https://zenodo.org/record/2634308#.X9jYwWRKj0u
Tree was converted with nexus2phyjson (compiled from the repository)‚