############################################################################################################################ # Decisive Datasets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects # - Supplementary File Archives - ############################################################################################################################ This README was written on 2013-09-06. If you have any questions regarding the nature of our data, please feel free to contact Karen Meusemann (mail AT karen-meusemann.de) and / or Bernhard Misof (b.misof.zfmk AT uni-bonn.de) ================================================================================== Dell'Ampio E, Meusemann K, Szucsich NU, Peters RS, Meyer B, Borner J, Petersen M, Aberer AJ, Stamatakis A, Walzl MG, von Haeseler A, Minh BQ, Ebersberger I, Pass G, and Misof B. 2013. Decisive Datasets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects. ================================================================================== Included Archives: NOTE: in all files *.matrix the value "-1" indicates OGs that are absent in this datamatrix! Supplementary File Archive 1. Archive of the concatenated alignment (supermatrix) including partition table and datamatrix with values of treelikeness of the complete dataset. The following files are included: 1. "supermatrix_complete.fas": supermatrix in FASTA format including 1,866 orthologous genes (OGs, masked amino acid gene alignments) and 73 taxa. 2. "supermatrix_complete.partition": partition table in plain text format 3. "supermatrix_complete.matrix": datamatrix with values of treelikeness in plain text format Supplementary File Archive 2. Archive of the concatenated alignment (supermatrix) including partition table and datamatrix with values of treelikeness of dataset M_Ento (rogue taxa pruned). Please refer to the publication for further explanations on the design of the dataset. The following files are included: 1. "M_Ento.fas": supermatrix in FASTA format including 117 orthologous, masked genes (OGs, masked amino acid gene alignments) and 72 taxa. 2. "M_Ento.partition": partition table in plain text format 3. "M_Ento.matrix": datamatrix with values of treelikeness in plain text format Supplementary File Archive 3. Archive of the concatenated alignment (supermatrix) including partition table and datamatrix with values of treelikeness of dataset SOS. Please refer to the publication for further explanations on the design of the dataset. The following files are included: 1. "SOS.fas": supermatrix in FASTA format including 253 orthologous, masked genes (OGs, masked amino acid gene alignments) and 62 taxa. 2. "SOS.partition": partition table in plain text format 3. "SOS.matrix": datamatrix with values of treelikeness in plain text format Supplementary File Archive 4. Archive of the concatenated alignment (supermatrix) including partition table and datamatrix with values of treelikeness of dataset SOSOMEGA. Please refer to the publication for further explanations on the design of the dataset. The following files are included: 1. "SOSOMEGA.fas": supermatrix in FASTA format including 174 orthologous, masked genes (OGs, masked amino acid gene alignments) and 62 taxa. 2. "SOSOMEGA.partition": partition table in plain text format 3. "SOSOMEGA.matrix"datamatrix with values of treelikeness in plain text format Supplementary File Archive 5. Archive of the concatenated alignment (supermatrix) including partition table and datamatrix with values of treelikeness of dataset M_Nono (rogue taxa pruned). Please refer to the publication for further explanations on the design of the dataset. The following files are included: 1. "M_Nono.fas": supermatrix in FASTA format including 51 orthologous, masked genes (OGs, masked amino acid gene alignments) and 72 taxa. 2. "M_Nono.partition": partition table in plain text format 3. "M_Nono.matrix": datamatrix with values of treelikeness in plain text format Supplementary File Archive 6. Archive of the concatenated alignment (supermatrix) including partition table and datamatrix with values of treelikeness of dataset M_Elli (rogue taxa pruned). Please refer to the publication for further explanations on the design of the dataset. The following files are included: 1. "M_Elli.fas": supermatrix in FASTA format including 35 orthologous, masked genes (OGs, masked amino acid gene alignments) and 70 taxa. 2. "M_Elli.partition": partition table in plain text format 3. "M_Elli.matrix": datamatrix with values of treelikeness in plain text format Supplementary File Archive 7. Archive of the concatenated alignment (supermatrix) including partition table and datamatrix with values of treelikeness of dataset M_DiCo (rogue taxa pruned). Please refer to the publication for further explanations on the design of the dataset. The following files are included: 1. "M_DiCo.fas": supermatrix in FASTA format including 31 orthologous, masked genes (OGs, masked amino acid gene alignments) and 69 taxa. 2. "M_DiCo.partition": partition table in plain text format 3. "M_DiCo.matrix": datamatrix with values of treelikeness in plain text format Supplementary File Archive 8. Archive of the 1,866 orthologous genes (OGs), unmasked and masked gene alignments. The following files are included: 1. *.fas: 1,866 files in fasta format (unmasked) [* -> OG-ID] 2. ALICUT_*.fas: 1,866 files in fasta format (masked) [* -> OG-ID] Supplementary File Archive 9. Assembly of EST data from Megajapyx sp. and Thermobia domestica used for orthology assignment. The following files are included: 1. "Megajapyx_sp_contig.fa": file in FASTA format with all contigs (nucleotide sequences) 2. "Thermobia_domestica_contig.fa": file in FASTA format with all contigs (nucleotide sequences)