### Analysis repository for: Evolutionary walks through flower color space driven by gene expression in Petunia and allies (Petunieae) #### Folders information **additional_raw_data** - contains raw data files not uploaded to the SRA, including HPLC peak tables and text file chromatograms **dataset_summary_statistics** - contains the tools to calculate the summary stats presented in the manuscript **DFR_structural_evolution** - contains the analysis of DFR amino acid subsitution in Plowmania nyctaginoides **molecular_evolution** - contains the analysis of dN/dS ratios for the flavonoid genes **pathway_gene_extraction** - contains the pipeline to extract flavonoid genes and merge homologs **phyloCCA** - contains the phylogenetic Canonical Correlation Analysis of gene expression and pigmentation **phyloPCA** - contains the phylogenetic Principal Components Analyses of gene expression and pigmentation **salmon_expression_quantification** - contains the pipeline for quantifying and summarizing flavonoid gene expression **species_tree_reanalysis** - contains the pipeline to add Fabiana australis into the species tree and ultrametricize the new tree **SRA_metadata** - contains the metadata for the RNA-seq data uploaded to the SRA (BioProject PRJNA746328) **stochastic_mapping** - contains the Stochastic Mapping analysis for ancestral state reconstruction of pigmentation **tanscriptome_assembly_scripts** - contains the scripts used to perform de novo transcriptome assemblies **transcriptome_assemblies_CDS** - contains the assembled transcriptomic CDS for all 60 species and some corresponding quality statistics