GAP is an R implementation of a neural network for predicting genotype-phenotype associations from gaps in multi-species sequence alignments (Islam et al. 2025).

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 (Campelo dos Santos et al. 2024).

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).