Method matters in gene family evolution

• DOI: 10.5281/zenodo.5091740
• Publication Date: 2021-07-12
• Authors: Begum, Tina; Serrano-Serrano, ...; Robinson-Rechavi,...

“Timetree_10000sim_100tip.rda” file of this repository contains simulated 10000 time trees, each with 100 tips. These trees were used further to generate substitution rates trees, and to calibrated time trees with different proportions of duplications. “Calibration_tree_painted_0.1_0.02two_ways_new.rda”, “Calibration_tree_painted_0.2_0.02two_ways_new.rda”, and “Calibration_tree_painted_0.8_0.02two_ways_new.rda” files contain simulated time calibrated gene trees using proportions of duplications of 0.1, 0.2, and 0.8, respectively. “Simulated_trees_from_empirical_data.Rdata” and “Simulated_trees_all_from_empirical_data.Rdata” files, which contain simulated gene trees using empirical data parameters to verify the results of all three pure simulation models of this study. “Time_dependent_1.2times_empirical_data.Rdata” and “Time_dependent_5times_empirical_data.Rdata” files contain the results of the “Time dependent trait acceleration model” using 1.2 and 5 times higher trait acceleration following gene duplications, respectively. “Simulated_trees_for_model2_from_empirical_data_parameters.Rdata” file contains simulated gene trees for all possible hypothetical scenarios to verify the result of “Rates of sequence and trait evolution model”. “seq_n_trait_acc_model_with_empirical_data_params.Rdata” file contains the results of the “Rates of sequence and trait evolution model” using empirical data parameters. “Jump_model_simulation_with_empirical_data_parameters.Rdata” file contains the results of the “Asymmetric trait jump model” using empirical data parameters. All the required scripts, and functions used in this study are available on GitHub: https://github.com/tbegum/Method-matters-in-gene-family-evolution.