CLOUD is an R implementation of DeGiorgio and Assis' (2020) multi-layer neural network for classifying duplicate gene retention mechanisms and predicting their evolutionary parameters from gene expression data in two species.

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

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