convergent-evolution

Analyzing combinations of codon substitution histories

CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology

Comparative molecular life history of spontaneous canine and human gliomas. Amin et al. Cancer Cell 2020

Tools for analysing discrete data in a phylogenetic context, e.g. discrete morphological phylogenetic characters. Calculate relative homoplasy, explore phylomorphospace. Integrates functions from 'ape', 'phangorn' and 'phytools'.

Unsupervised detector for molecular convergent evolution using ESM-2 embeddings and a homology gate — finds non-homologous proteins with identical function, no phylogeny needed.

One carbon-joining reaction, one downstream decision: how the same chemistry builds a storage fat and a DNA-poisoning anticancer antibiotic.

Scripts related to the mansucript "Convergent evolution in Afrotheria and non-afrotherians demonstrates high evolvability of the mammalian inner ear" (Grunstra et al.)