Phylogenetic comparative methods are problematic when applied to gene trees with speciation and duplication nodes: correcting for biases in testing the ortholog conjecture

This repository contains “manuscript_dunn.RData” file, which is reproduced by using the files and scripts of Dunn et al. (Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A (2018) Pairwise comparisons across species are problematic when analyzing functional genomic data. Proc Natl Acad Sci U S A 115: E409–E417. doi:10.1073/pnas.1707515115). In this repository, we also supplied “Data_TMRR_latest.rda” file, containing the results generated by using our own scripts. Our scripts are available on GitHub: https://github.com/tbegum/Testing_the_ortholog_conjecture.