├── LICENSE ├── README.md └── Scripts ├── 10_Recovery ├── Recovery_per_order.R ├── no_gap_length.csv └── total_length.csv ├── 11_Tanglegrams ├── 4782_ML_433_12_Family_bootstrap.tre ├── APG_IV.tre ├── family_assoc.csv └── tanglegrams.R ├── 1_Phylogenetic_inference ├── Root_gene_trees_sortadate.R ├── TreeToConstraints.pl ├── amas_per_gene.sh ├── amas_summary.sh ├── begin_bigtree.sh ├── begin_combined_analysis.sh ├── begin_ordinal_iteration.sh ├── check_direction.py ├── colate_ordinal_files.sh ├── combined_aggregate_treeshrink_output.sh ├── combined_astral.sh ├── combined_branch_length.sh ├── combined_check_arrays.sh ├── combined_fasttree.sh ├── combined_launch_arrays.sh ├── combined_launch_fasttree.sh ├── combined_mafft.sh ├── combined_mafft_low_mem.sh ├── combined_mafft_new_dir.sh ├── combined_mafft_new_dir_low_mem.sh ├── combined_mafft_orphans.sh ├── combined_prepare_calibration.sh ├── combined_prepare_constraints.sh ├── combined_sortadate.sh ├── combined_standards.sh ├── combined_treeshrink.sh ├── concat_misdirection_files.sh ├── distribute_seqs.sh ├── estimate_branch_lengths.sh ├── gene_list.txt ├── gene_list_sorted.txt ├── get_previous_mafft_mem.sh ├── launch_ordinal.sh ├── launch_treeshrink_i2.sh ├── makemergetable.rb ├── makemergetable.sh ├── ordinal_astral.sh ├── ordinal_astral_gpu.sh ├── ordinal_backup.sh ├── ordinal_check_mafft_iqtree.sh ├── ordinal_continue_iqtree.sh ├── ordinal_mafft.sh ├── ordinal_mafft_iqtree.sh ├── ordinal_mafft_only.sh ├── ordinal_parameters.sh ├── ordinal_sacct.sh ├── ordinal_treeshrink.sh ├── ordinal_treeshrink_astral.sh ├── outgroup.txt ├── outgroups.txt ├── prepare_branch_lenght_alignments.R ├── prune_tree_to_alignment.R ├── remove_backbone_outliers.R ├── root_by_vector.R ├── root_gene_trees.R ├── sequence_handler.py ├── sortadate.sh ├── summary.sh ├── sync_big_results.sh └── tips.csv ├── 2_Calibration ├── README.txt └── input_for_treePL.treePL ├── 3_Figure_1 ├── New_Calibrations.csv └── circle_tree.R ├── 4_Figure_2 └── Figure_2.R ├── 5_Lineage_specific_diversification_rate_analyses ├── README.txt ├── bamm_input.bamm ├── branch_specific.Rev ├── family_sampling_proportions.tsv └── set_priors.R ├── 6_Time_dependent_diversification_rate_analysis ├── bayes_factor_comparison │ ├── README.txt │ ├── episodic_model_extinction_variable_bf.Rev │ ├── episodic_model_nothing_variable_bf.Rev │ ├── episodic_model_speciation_variable_bf.Rev │ └── sampling_fractions.Rev └── exploratory_analyses │ ├── README.txt │ ├── derive_inference_windows.R │ ├── episodic_model_extinction_variable_young_tree.Rev │ ├── episodic_model_nothing_variable_young_tree.Rev │ ├── episodic_model_speciation_variable_old_tree.Rev │ ├── episodic_model_speciation_variable_young_tree.Rev │ └── sampling_fractions.Rev ├── 7_estimation_of_sampling_through_time ├── README.txt └── percentage_missing_with_sim_v2.r ├── 8_conflict_and_diversification_simulations ├── README.txt └── coalescent_sim.R ├── 9_Clade_ages ├── Age_comparsion.pdf ├── 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