CLOUD

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.

CLOUD.zip

CDROM

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.

Manual

CDROM.zip

Bridges

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

It is freely available for download on GitHub.