CAGEE analyzes changes in global or sample- or clade-specific gene expression taking into account phylogenetic history, and provides a statistical foundation for evolutionary inferences.
The program (v1.0) uses Brownian motion to model gene expression changes across a user-specified phylogenetic tree.
The reconstructed distribution of counts and their inferred evolutionary rate
conda create -n cagee -c bioconda cagee
If you would like to build from source code, download the latest release from the release page, and see the manual for details. CAGEE depends on CMake, Boost, and Eigen for building.
There is also a Docker container available.
See the manual for quick start and detailed usage instructions.