CLOUDe is an R implementation of three machine learning methods for predicting evolutionary targets and parameters of gene deletion events from expression data in two species.

ROBRT is an R implementation of robust L1, M, S, and MM phylogenetic independent contrast regression estimators for evaluating trait associations on phylogenetic trees (Adams et al. 2023).

PiXi is an R implementation of three machine learning methods for predicting gene expression divergence between single-copy orthologs in two species (Piya et al. 2023).

CLOUD is an R implementation of a neural network for predicting duplicate gene retention mechanisms and their evolutionary parameters from expression data in two species (DeGiorgio and Assis 2021).

CDROM is an R implementation of a decision tree for classifying duplicate gene retention mechanisms from gene expression data in two species (Assis and Bachtrog 2013, Perry and Assis 2016).

Bridges is a C implementation of a heuristic search algorithm for identifying local similarities in long DNA sequences (Assis and Kondrashov 2010).