Data from: The effect of copy number hemiplasy on gene family evolution

# Overview We provide here the simulation scripts and datasets to reproduce the simulation results of the paper **The effect of copy number hemiplasy on gene family evolution**. Based on a species tree consisting of 16 fungal genomes, we simulate comparable gene trees under MLMSC-II and SimPhy. The simulated gene trees are compared against various summary statistics including the number of genes, number of species, number of surviving duplications, and balance indices such as Colless index and Sackin index. The simulated gene trees are also used for comparing the performance of the quartet-based species tree inference methods ASTRAL and ASTRAL-Pro under both models. ## appendix.pdf This is a summary of the supplementary materials of the paper **The effect of copy number hemiplasy on gene family evolution**, including the following topics: * **Supplementary Figures** * **Additional WFD Simulations** * **Comparisons of Balance Indices** * **ASTRAL with Single-labelled Gene Trees** * **ASTRAL with Different Number of Input Gene Trees** * **ASTRAL with Non-Equal Duplication and Loss Rates** * **Simulations on the Primate Tree** ## data\_analysis This directory stores all simulated data and R scripts for data analysis and plots. The simulated gene trees are stored in the following directories: * **data_analysis/mlmsc_tree**: gene trees simulated using MLMSC-II * **data_analysis/symphy_tree**: gene trees simulated using SimPhy Note that we only keep 1000 gene trees for each set of parameters for demonstration, but 100000 gene trees are used in the original simulation. The bacis summary statistics of the simulated gene trees (e.g., n_dups, n_genes, n_species) are stored in the following directories: * **data_analysis/mlmsc_summary**: bacis summary statistics of the gene trees simulated using MLMSC-II * **data_analysis/symphy_summary**: bacis summary statistics of the gene trees simulated using SimPhy The results of species tree inference are stored in the following directories: * **data_analysis/astral_mlmsc**: results of species tree inference using gene trees simulated using MLMSC-II * **data_analysis/astral_symphy**: results of species tree inference using gene trees simulated using SimPhy For more information, please refer to **data_analysis/README.md**. ## mlmsc\_bin This directory contains all the scripts for simulating gene trees using MLMSC-II, and performing species tree inference (by ASTRAL and ASTRAL-Pro) on the simulated gene trees. To install ASTER/ASTRAL-Pro, do ``` git clone https://github.com/chaoszhang/ASTER.git ``` and follow the instructions. The scripts expect the ASTRAL/ASTRAL-Pro binary to be in **./ASTER/bin/astral-pro** When simulating trees, gene trees are stored in **mlmsc_bin/output**: * **gene_tree.newick**: a list of multi-labelled gene trees, each containing of all simulated homologous genes * **random_tree.newick**: a list of single-labelled gene trees, each containing only one --randomly-chosen-- gene per species * **summary.txt**: summary statistics including the number of surviving duplications (n_d), number of genes (n_genes), and number of species (n_species) When inferring specie trees, species tree inference results are stored in **mlmsc_bin/astral_summary_fungi**: * **mlmsc_random.txt**: ASTRAL results * **mlmsc_gene.txt**: ASTRAL-Pro results For more information, please refer to **mlmsc_bin/README.md**. ## simphy\_bin This directory is for simulating gene trees using SimPhy, and performing species tree inference (by ASTRAL and ASTRAL-Pro) on the simulated gene tree. Simulated gene trees are stored in **simphy_bin/output**: * **gene_tree.newick**: a multi-labelled gene tree consisting of all homologous genes * **random_tree.newick**: a single-labelled gene tree in which only one gene is randomly selected for each descendant species * **summary.txt**: summary statistics including the number of surviving duplications (n_d), number of genes (n_genes), and number of species (n_species) Species tree inference results are stored in **simphy_bin/astral_summary_fungi**: * **simphy_random.txt**: ASTRAL results * **simphy_gene.txt**: ASTRAL-Pro results For more information, please refer to **simphy_bin/README.md**. ## WFDL\_bin This directory is for simulating the fraction of higher order duplications using the Wright-Fisher model with duplication and loss (WFDL). For more information, please refer to **WFDL_bin/README.md**.