CAGEE 1.2 is now available!
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 new version supports likelihood estimation as a gamma curve and input data that is expressed as ratios.
Download from here:
Release 1.2 · hahnlab/CAGEE
Applications of machine learning in phylogenetics
"Supervised machine learning approaches that rely on simulated training data have been used to infer tree topologies and branch lengths, to select substitution models, and to perform downstream inferences of introgression and diversification...We review how researchers have used several promising machine learning approaches to make phylogenetic inferences."
#MachineLearning #Phylogenetics
Published version of CAGEE!
Here, we present a new software package (Computational Analysis of Gene Expression Evolution [CAGEE]) for inferring patterns of increases and decreases in gene expression across a phylogenetic tree, as well as the rate at which these changes occur. CAGEE can calculate genome-wide rates of gene expression, along with ancestral states for each gene.
#phylogenetics #bioinformatics
Our new software is out!
"Here, we present a new software package (CAGEE) for inferring patterns of increases and decreases in gene expression across a phylogenetic tree, as well as the rate at which these changes occur. In contrast to previous methods that treat each gene independently, CAGEE can calculate genome-wide rates of gene expression, along with ancestral states for each gene."
#phylogenetics #software #OpenSource
