Data for: Well-resolved phylogeny reveals multiple origins of keel flowers during the diversification of papilionoid legumes

This folder contains supplementary data from Cai et al (in review) regarding the phylogenomic investigation of the papilionoideae legumes. The following data is included.Data S1 DNA alignments and maximum likelihood phylogenies inferred for the 1,456 low copy nuclear genes used in this study. The alignments are inferred using the MAFFT-linsi algorithm. The gene trees are reconstructed using IQTREE and branch support is evaluated with 1000 ultrafast bootstrap replication. Species names and their corresponding ID are provided in sp_ID.csv. The list of 672 loci used to generated the concatenated matrix for species tree estimation is provided in G672_len900_sp227.list.Data S2 Distribution of 21-mer frequency in 32 species with genome skimming data. The 21-mer frequency is inferred from Jellyfish v2.3.0 to estimate sequencing coverage. The species names and ID for each accession is provided in Species_ID.tsv. See Table S1 in the main text for voucher information.Data S3 Gene and site concordance factors of the Papilionoideae phylogeny. The species tree and concatenated alignment of the 672-gene dataset were used as inputs in IQ-TREE to calculate these concordance factors. The gene concordance factors (gCF) and site concordance factors (sCF) are annotated as node labels in the nexus formatted phylogeny.