README This DRYAD package contains files that relate to: Akito Y. Kawahara and Jesse W. Breinholt (2014) Phylogenomics provides strong evidence for the relationships of butterflies and moths. Proceedings of the Royal Society B, Biological Sciences Please cite this publication, the DRYAD accession, and Genbank SRA accession number when using any of the data or core ortholog set from this package. This DRYAD data package includes 46 files, in addition to this README file: taxa_list.txt: List of Sample ID's used in nexus files, species names, Assembly File Name, and Genbank SRA in tab-delimited text LEP1-COS.tar.gz: This compressed directory contains the HaMStR (Ebersberger et al. 2009: http://sourceforge.net/projects/hamstr/) formatted core-ortholog set we compiled to analyze the phylogeny of Lepidoptera in Kawahara and Breinholt (2014). See the file Taxon_list_readme.txt inside the compressed directory and Kawahara and Breinholt (2014) for more information about this core-ortholog set. final_soap_SW130206.fa: Assembly of Nemophora sp. from Genbank SRA accession #SRR1299782, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120096B.fa: Assembly of Eacles sp. from Genbank SRA accession #SRR1299435, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120016.fa: Assembly of Therinia lactucina from Genbank SRA accession #SRR1299418, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120049B.fa: Assembly of Adhemarius daphne from Genbank SRA accession #SRR1299394, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_Xter2.fa: Assembly of Xylophanes tersa from Genbank SRA accession #SRR1298384, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_Callid.fa: Assembly of Pterodecta felderi from Genbank SRA accession #SRR1299369, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120022.fa: Assembly of Morpheis mathani from Genbank SRA accession #SRR1299214, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_SW130197.fa: Assembly of Dichomeris sp. from Genbank SRA accession #SRR1299773, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_SW130007.fa: Assembly of Thubana sp. from Genbank SRA accession #SRR1300991, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_GNV120029.fa: Assembly of Macaria distribuaria from Genbank SRA accession #SRR1299213, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_GNV120032.fa: Assembly of Nemoria lixaria from Genbank SRA accession #SRR1299347, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120055B.fa: Assembly of Nothus lunus from Genbank SRA accession #SRR1299318, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_SW130126.fa: Assembly of Lyssa zampa from Genbank SRA accession #SRR1299769, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_Pcit2.fa: Assembly of Phyllocnistis citrella from Genbank SRA accession #SRR1299751, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120028B.fa: Assembly of Aepytus sp. from Genbank SRA accession #SRR1299317, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120070B.fa: Assembly of Artace sp. from Genbank SRA accession #SRR1299316, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120046B.fa: Assembly of Lacosoma ludolpha from Genbank SRA accession #SRR1299212, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_SW130232.fa: Assembly of Eudocima salaminia from Genbank SRA accession #SRR1300148, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_SW130103.fa: Assembly of Anigraea sp. from Genbank SRA accession #SRR1299755, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_SW130224.fa: Assembly of Manoba major from Genbank SRA accession #SRR1300145, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120015.fa: Assembly of Notoplusia minuta from Genbank SRA accession #SRR1299746, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120122.fa: Assembly of Macrosoma sp. from Genbank SRA accession #SRR1299306, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_GNV120020.fa: Assembly of Hylephila phyleus from Genbank SRA accession #SRR1299296, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_GNV139000.fa: Assembly of Megathymus yuccae from Genbank SRA accession #SRR1299752, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_GNV120025.fa: Assembly of Hemiargus ceraunus from Genbank SRA accession #SRR1299274, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120077.fa: Assembly of Semomesia campanea from Genbank SRA accession #SRR1299211, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_SRR850324.fa: Assembly of Papilio glaucus from Genbank SRA accession #SRR850324 , using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_SRR850327.fa: Assembly of Papilio polytes from Genbank SRA accession #SRR850327 , using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_GNV120027.fa: Assembly of Lantanophaga pusillidactyla from Genbank SRA accession #SRR1299210, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_SRR64791_.fa: Assembly of Cnaphalocrocis medinalis from Genbank SRA accession #SRR647910 - SRR647915 , using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120071B.fa: Assembly of Myelobia sp. from Genbank SRA accession #SRR1299267, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_GNV139006.fa: Assembly of Pseudothyris sepulchralis from Genbank SRA accession #SRR1299495, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120079.fa: Assembly of Zeuzerodes maculata from Genbank SRA accession #SRR1299209, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_SRR803483.fa: Assembly of Grapholita dimorpha from Genbank SRA accession #SRR803483 , using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_GNV129007.fa: Assembly of Urodus parvula from Genbank SRA accession #SRR1299750, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120035.fa: Assembly of Dalcera abrasa from Genbank SRA accession #SRR1299208, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. final_soap_FG120024.fa: Assembly of Megalopyge tharops from Genbank SRA accession #SRR1299217, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details. Kawahara_Breinholt_2014_26taxa_465loci_aa.nex: Nexus file containing 465 genes for 26 taxa. See taxa_list.txt for species names of each taxon, this is an amino acid nexus file with a CHARSET that defines each gene. The data was trimmed using ALICUT/ALISCORE (http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/Aliscore/index.en.html). Gene names correspond to gene numbers in the LEP1-COS core ortholog database included in this DRAYD package. For further information see text and supplementary tables in Kawahara and Breinholt (2014). Kawahara_Breinholt_2014_26taxa_465loci_aa.model.txt: RAxML formatted partitioning and model file. This partitioning file was used to analyze data in Kawahara_Breinholt_2014_26taxa_465loci_aa.nex. 198 partitions and amino acid models defined by partitionfinder (Lanfear et al 2012). See text and supplementary text in Kawahara and Breinholt (2014) for more details. Kawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.nex: Nexus file containing codon position 1 & 2 for 465 genes for 26 taxa. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. The nucleotide data was trimmed 3 codons at a time with ALICUT/ALISCORE (http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/Aliscore/index.en.html), synonymous signal removed using degen v1.4 Perl script (http://www.phylotools.com), and the third codon has been removed. Gene names correspond to gene numbers in the LEP1-COS core ortholog database included in this Dryad package. For further information see text and supplementary tables in Kawahara and Breinholt (2014). Kawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.model.txt: RAxML formatted partitioning file. This partitioning file was used to analyze data in Kawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.nex. 178 partitions defined by partionfinder (Lanfear et al 2012). See text and supplementary text in Kawahara and Breinholt (2014) for more details. Kawahara_Breinholt_2014_46taxa_2696loci_Degen_nt12.nex: Nexus file containing codon position 1 & 2 for 2969 genes for 46 taxa. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. The nucleotide data was trimmed 3 codons at a time with ALICUT/ALISCORE (http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/Aliscore/index.en.html), synonymous signal removed using degen v1.4 Perl script (http://www.phylotools.com), and the third codon has been removed. Gene names correspond to gene numbers in the LEP1-COS core ortholog database included in this Dryad package. For further information see text and supplementary tables in Kawahara and Breinholt (2014). Kawahara_Breinholt_2014_46taxa_2696loci_Degen_nt12.model.txt: RAxML formatted partitioning and model file. This partitioning file was used to analyze data in Kawahara_Breinholt_2014_47taxa_2696loci_Degen_nt12.nex. Two partitions by codon position. See text and supplementary text in Kawahara and Breinholt (2014) for more details. Kawahara_Breinholt_2014_46taxa_2696loci_aa.nex: Nexus file containing 2969 genes for 46 taxa. See taxa_list.txt for species names of each taxon, this is a amino acid nexus file with a CHARSET that defines each gene. The data was trimmed using ALICUT/ALISCORE (http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/Aliscore/index.en.html). Gene names correspond to gene numbers in the LEP1-COS core ortholog database included in this Dryad package. For further information see text and supplementary tables in Kawahara and Breinholt (2014). For questions regarding these data, contact Jesse Breinholt at jessebreinholt@gmail.com or Akito Kawahara at kawahara@flmnh.ufl.edu