README ————————————————————————————————— ————————————————————————————————— 1) Supplementary Files of phylogenetic analyses of proteins involved in beta-oxidation, (Suppl. Figures 5-12) ——————————————————————————————————————————————————————————————————————————————————— For each tree, the following data files are included: *.fasta -- unaligned sequences *.ma.fasta -- aligned sequences with mafft *.ma.bm.fasta -- aligne sequences with mafft trimmed with BMGE *.treefile -- IQTREE tree file *.log -- IQTREE log file For COG1960 clade 2 hmmalign was used instead of mafft. A concatenated profile of PFAM ids: Acyl-CoA_dh_N Acyl-CoA_dh_M Acyl-CoA_dh_1 was used to generate COG01960clade2_hmmalign_trim.fasta 2) Supplementary Files of phylogenetic analyses of all other single protein trees (Figure 2 and Suppl. Figures 14-18) ——————————————————————————————————————————————————————————————————————————————————— For each tree, the following data files are included *_LINSi.fst - — untrimmed alignments *_BMGE30.fst or *_BMGE.phy or *_gappyout.fst — — trimmed alignments *.treefile — — IQTREE tree file *.log — — IQTREE log file 3) Supplementary files for concatenated phylogenies (Figure 3 and Supplementary Data 1-3) ——————————————————————————————————————————————————————————————————————————————————— For each tree, the following data files are included *.fasta — concatenated alignments *.treefile — concatenated phylongies 4) Scripts ————————————————————————————————— Scripts that were used to parse the annotations or to analyse the single protein trees 5) Files ————————————————————————————————— Table listing the phylogenetic marker genes used to construct the concatenated phylogenies according to Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353-358, doi:10.1038/nature21031 (2017).