This repository contains phylogenetic data matrices, multiple sequence alignments, phylogenetic trees, supplementary figures and tables, R codes, and the custom Perl scripts used in this study. 1) Each folder corresponds to each topic in our study. 2) Example_GLS&GQS_caculation can guide us to calculate gene-wise log-likelihood score (GLS) and gene-wise quartet score (GQS) for every gene Please let me know if you have any question about them. email: xingxingshen@zju.edu.cn