14 projects
bdpn
Estimation of BDPN parameters from phylogenetic trees.
phylodeep
Phylodynamic paramater and model inference using pretrained deep neural networks.
pastml
Ancestral character reconstruction and visualisation for rooted phylogenetic trees.
treesimulator
Simulation of rooted phylogenetic trees under a given Multitype Birth–Death model.
geo-subsampler
Subsampling of rooted phylogenetic trees using phylogenetic diversity and location proportions.
phylodeep-data-bdss
Data needed for CI computation with Birth-Death model with superspreading (BDSS) in [PhyloDeep](https://github.com/evolbioinfo/phylodeep).
pybdei
Fast and accurate epidemiological parameter estimation from phylogenetic trees with the Birth-Death Exposed-Infectious (BDEI) model.
phylodeep-data-bdei
Data needed for CI computation with Birth-Death Exposed-Infectious (BDEI) model in [PhyloDeep](https://github.com/evolbioinfo/phylodeep).
phylodeep-data-bd
Data needed for CI computation with Birth-Death (BD) model in [PhyloDeep](https://github.com/evolbioinfo/phylodeep).
jphmm-tools
Tools for extracting information from jpHMM (http://jphmm.gobics.de) output.
cytopast
Visualisation of PastML trees.
sbml_vis
SBML zoomable visualization utilities.
mod_sbml
Utilities for working with metabolic models in SBML format.
sbml_generalization
Knowledge-based generalization for metabolic models in SBML format.
