17 projects
bdext
Estimation of BDEISS-CT parameters from phylogenetic trees.
bdct
Maximum likelihood estimation of BD, BD-CT(1) and BDSKY parameters from phylogenetic trees.
treesimulator
Simulation of rooted phylogenetic trees under a given Multi-Type Birth–Death model, with or without Contact Tracing, with or without a Skyline.
pastml
Ancestral character reconstruction and visualisation for rooted phylogenetic trees.
treesumstats
Encoding phylogenetic trees with summary statistics.
bdpn
Estimation of BDPN parameters from phylogenetic trees.
phylodeep
Phylodynamic paramater and model inference using pretrained deep neural networks.
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.
