EvoDA is an R program that implements discriminant analysis for evolutionary model selection (Lozano et al. 2026).

ANDES is a Python and R program that implements six unsupervised machine learning algorithms for identifying anomalous genomic regions from SNPs using functional data analysis (Kanjilal et al. 2025).

GAP is a Python and R program that implements a neural network for predicting genotype–phenotype associations from gaps in multi-species sequence alignments (Islam et al. 2025).

CLOUDe is an R program that implements four machine learning algorithms 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 program that implements 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 program that implements three machine learning algorithms for predicting gene expression divergence and its evolutionary parameters between single-copy orthologs in two species (Piya et al. 2023).

CLOUD is an R program that implements three machine learning algorithms for predicting duplicate gene retention mechanisms and evolutionary parameters from expression data in two species (DeGiorgio and Assis 2021).

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

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