"Angiosperms353" contains analyses and outputs pertaining to the Angiosperms353 dataset
		"alignments" contains gene alignments used for final gene tree estimation and the concatenated alignment for molecular branch length estimation
		"assembled_seqs" contains assembled sequences
		"gene_trees" contains final estimated gene trees
		"ASR_life_history.R" is the script used to perform life reconstruction and discrete character model comparison
		"asr_life_history_model_comparison.txt" shows comparison of different models for life history reconstruction
		"astral_input.txt" is the input for astral, with a couple of final processing steps like collapsing poorly supported branches
		"climate_reconstruction.R" shows the script used for l1ou analyses
		"dated.tre" is the dated Angiosperms353+ITS phylogenetic tree
		"final_353_sp_tree_mol_bl.tre" is the Angiosperms353+ITS phylogenetic tree with molecular branch lengths
		"generate_mono_sampling_props.r" is the script used to define clade specific sampling fractions
		"initial_353_sp_tree_astral_bl.tre" is the Angiosperms353+ITS species tree estimated in astral
		"l1ou_model_test_summary.out" summarises the parameter estimates and models compared by l1ou
		"rax_part.txt" is the partition file for molecular branch length estimation
		"raxml_input.ml" is the input used with raxml
		"template_diversification.bamm" is the input file for the main analysis in bamm
		"treePL_input.r8s" is the input for divergence time estimation in treePL

"Bioclimatic_and_life_history_database"
		"data_transformed_pca1.csv" has the transformed climatic data
		"full_climate_means.csv" has the untransformed climatic data
		"life_history_table.csv" has the life history matrix
	
"Chloroplast" has all the scripts pertaining to analysis on the chloroplast data
		"alignments" contains gene alignments used for final gene tree estimation and the concatenated alignment for molecular branch length estimation
		"assembled_seqs" contains assembled sequences
		"gene_trees" contains final estimated gene trees
		"ASR_life_history.R" is the script used to perform life reconstruction and discrete character model comparison
		"asr_life_history_model_comparison.txt" shows comparison of different models for life history reconstruction
		"astral_input.txt" is the input for astral, with a couple of final processing steps like collapsing poorly supported branches
		"climate_reconstruction.R" shows the script used for l1ou analyses
		"cp_its_dated.tre" is the dated tree with chloroplast and its data
		"cp_its_older_maximum_tree.tre" is the dated tree with chloroplast and its data and a 125Ma max at the root nodes
		"cp_its_remove_influential_fossils.tre" is the dated tree with chloroplast and its data and the five likely higly influential fossil calibrations removed
		"final_cp_its_sp_tree_mol_bl.tre" is the molecular branch length tree with chloroplast and its data
		"generate_mono_sampling_props_for_bamm.r" is the script used to define clade specific sampling fractions
		"initial_cp_its_sp_tree_astral_bl_tree.tre" is the astral tree with cp and its data
		"initial_cp_only_sp_tree_astral_bl.tre" is the astral tree with just chloroplast data
		"initial_cp_only_sp_tree_mol_bl.tre" is the molecular branch length tree with just chloroplast data
		"model_test_summary_l1ou_chloroplast.out" summarises the parameter estimates and models compared by l1ou in the chloroplast only tree
		"model_test_summary_l1ou_chloroplast_its.out" summarises the parameter estimates and models compared by l1ou in the chloroplast and its tree
		"rax_part.txt" is the partition file for molecular branch length estimation
		"raxml_input.ml" is the input used with raxml		
		"template_diversification.bamm" is the input file for the main analysis in bamm
		"treePL_input.r8s" is the input for divergence time estimation in treePL

"Target_files" has target files for chloroplast and its	
	
“Transcriptome” contains analyses and outputs of transcriptomic data.
		“alignment_for_molecular_branch_length_estimation” contains concatenated alignment for estimating molecular branch lengths in RAxML.
		"assembled_sequences" contains assembled homolog sequences
		"final_ortholog_trees" contains ortholog trees used for analysis in astral
		"homolog_alignments" contains aligned homolog sequences used to estimate homolog_trees
		"homolog_trees" contains estimated homolog trees
		"ortholog_alignments" contains aligned ortholog sequences
		"calculation_for_KS_plot.py" contains script for calculating KS distances between paralogous pairs
		"duplication_analysis_input.txt" contains the input for performing gene duplication analysis in phyparts
		"final_species_tree_with_molecular_branch_lengths.tre" is the species tree topology with molecular branch lengths estimated in raxml
		"initial_species_tree_astral_branch_lengths.tre" is the species tree estimated by astral, with astral branch lengths
		"match_up_tips_to_taxon_name.csv" enables accession numbers to be matched up to taxon names
		"rax_part.txt" is the partition file used in raxml
		"raxml_input_for_mol_br_len_estimation.ml" is the input for estimating molecular branch lengths in raxml
		"species_tree_estimation_astral.txt" is the species tree estimation step done in astral, with a couple of final processing steps (collapsing poorly supported nodes etc. )