Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics Keith M. Bayless1,2,3,13*, Michelle D. Trautwein3*, Karen Meusemann2,4,5, Seunggwan Shin1,6, Malte Petersen7, Alexander Donath4, Lars Podsiadlowski4, Christoph Mayer4, Oliver Niehuis5, Ralph S. Peters8, Rudolf Meier9,10, Sujatha Narayanan Kutty,9,11, Shanlin Liu12, Xin Zhou12, Bernhard Misof4, David K. Yeates2, Brian M. Wiegmann1 BMC Biology BMCB-D-20-00520 #Alignment matrix for Analysis 1- 3145 gene partitions, amino acids 70taxa_aa_part_unred_NOREF_FcC_smatrix.rename.phy #Gene partitions for Analysis 1- 3145 gene partitions, amino acids 70taxa_aa_part_unred_partitions.txt #Alignment matrix for Analyses 2,3,4- 1130 gene partitions, amino acids 70taxa1130genesDATArename.phy #Gene partitions for Analyses 2,3,4,6- 1130 gene partitions, amino acids 70taxa1130genesPARTITIONS.txt #PartitionFinder list of merged partitions for Analyses 2,3,4,6 -1130 genes in 132 partitions, amino acids 70taxaAA_1130g_132part_partitionfinder.txt #Alignment matrix for Analysis 5- reduced to sites with >80% coverage 70taxa2_aa.alistat80mask.rename.reorder.phy #Alignment matrix for Analysis 7- 3145 genes, nucleotides, all three codon positions. Only first and second codon positions included in analyses NT70taxa123pos_3145genes.phy #Gene partitions for Analysis 7- 3145 gene partitions, nucleotides, all three codon positions. Only first and second codon positions included in analyses NT70taxa123pos_3145genessupermatrix.nt.genes.final.charset #Alignment matrix for Analysis 8- 1130 gene partitions, nucleotides, all three codon positions. Only first and second codon positions included in analyses NT70taxa123_1130genes.phy #Gene partitions for Analysis 8- 1130 gene partitions, nucleotides, all three codon positions. Only first and second codon positions included in analyses NT70taxa123pos_1130supermatrix.nt.genes.final.charset 43.59 kB #PartitionFinder list of merged partitions for Analysis 8- 1130 genes, 736 partitions, nucleotides NT70taxa_1130g_736part_partitionfinder.txt