Software
TraitBlender is a Blender add-on for generating synthetic museum-style image and 3D mesh datasets. From theoretical or empirical morphospaces, it simulates taxa on phylogenies and renders standardized specimens in bulk—useful when benchmarks need ground-truth evolutionary processes.
PhyloNN uses restructured autoencoders and multi-task learning to incorporate evolutionary information such as phylogeny and ontogeny into deep learning models for phenotypic data. The goal is to ground high-dimensional or raw datasets in biological structure rather than treating morphology as an unstructured prediction problem.
RPhenoscate incorporates biological knowledge into comparative analyses through ontologies: knowledge graphs that specify hierarchical relationships between traits. This helps ensure that statistical models reflect biologically meaningful assumptions about how characters relate to one another.
SISRS (Site Identification from Short Read Sequences) is a phylogenomic pipeline for identifying informative sites and inferring orthologous sequences from short-read genomic data.