Data from: Phylogenomics provides strong evidence for the relationships of butterflies and moths

Kawahara AY, Breinholt JW

Date Published: June 5, 2014

DOI: http://dx.doi.org/10.5061/dryad.qd27g

 

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Title README.txt
Downloaded 53 times
Description This file contains descriptions of all the files associated with this Dryad package.
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Title LEP1-COS.tar.gz
Downloaded 37 times
Description 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.
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Title taxa_list.txt
Downloaded 37 times
Description taxa_list.txt: List of Sample ID's used in nexus files, species names, Assembly File Name, and Genbank SRA in tab-delimited text
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Title final_soap_SW130206
Downloaded 11 times
Description 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.
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Title final_soap_FG120096B
Downloaded 10 times
Description 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.
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Title final_soap_FG120016
Downloaded 11 times
Description 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.
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Title final_soap_FG120049B
Downloaded 11 times
Description 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.
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Title final_soap_Xter2
Downloaded 9 times
Description 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.
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Title final_soap_Callid
Downloaded 7 times
Description 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.
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Title final_soap_FG120022
Downloaded 6 times
Description 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.
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Title final_soap_SW130197
Downloaded 9 times
Description 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.
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Title final_soap_SW130007
Downloaded 11 times
Description 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.
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Title final_soap_GNV120029
Downloaded 10 times
Description 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.
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Title final_soap_GNV120032
Downloaded 9 times
Description 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.
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Title final_soap_FG120055B
Downloaded 7 times
Description 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.
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Title final_soap_SW130126
Downloaded 12 times
Description 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.
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Title final_soap_Pcit2
Downloaded 12 times
Description 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.
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Title final_soap_FG120028B
Downloaded 8 times
Description 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.
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Title final_soap_FG120070B
Downloaded 11 times
Description 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.
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Title final_soap_FG120046B
Downloaded 11 times
Description 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.
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Title final_soap_SW130232
Downloaded 13 times
Description 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.
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Title final_soap_SW130103
Downloaded 9 times
Description 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.
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Title final_soap_SW130224
Downloaded 8 times
Description 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.
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Title final_soap_FG120015
Downloaded 6 times
Description 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.
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Title final_soap_FG120122
Downloaded 12 times
Description 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.
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Title final_soap_GNV120020
Downloaded 10 times
Description 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.
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Title final_soap_GNV139000
Downloaded 10 times
Description 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.
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Title final_soap_GNV120025
Downloaded 14 times
Description 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.
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Title final_soap_FG120077
Downloaded 11 times
Description 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.
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Title final_soap_SRR850324
Downloaded 12 times
Description 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.
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Title final_soap_SRR850327
Downloaded 9 times
Description 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.
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Title final_soap_GNV120027
Downloaded 9 times
Description 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.
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Title final_soap_SRR64791_
Downloaded 13 times
Description 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.
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Title final_soap_FG120071B
Downloaded 11 times
Description 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.
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Title final_soap_GNV139006
Downloaded 8 times
Description 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.
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Title final_soap_FG120079
Downloaded 9 times
Description 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.
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Title final_soap_SRR803483
Downloaded 8 times
Description 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.
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Title final_soap_GNV129007
Downloaded 8 times
Description 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.
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Title final_soap_FG120035
Downloaded 13 times
Description 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.
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Title final_soap_FG120024
Downloaded 9 times
Description 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.
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Title Kawahara_Breinholt_2014_26taxa_465loci_aa.nex
Downloaded 23 times
Description 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).
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Title Kawahara_Breinholt_2014_26taxa_465loci_aa.model.txt
Downloaded 10 times
Description 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.
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Title Kawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.nex
Downloaded 17 times
Description 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).
Download Kawahara_Breinholt_2014_26taxa_465loci_De...12.nex (12.82 Mb)
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Title Kawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.model.txt
Downloaded 7 times
Description 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.
Download Kawahara_Breinholt_2014_26taxa_465loci_De...el.txt (17.24 Kb)
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Title Kawahara_Breinholt_2014_46taxa_2696loci_Degen_nt12.nex
Downloaded 18 times
Description 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).
Download Kawahara_Breinholt_2014_46taxa_2696loci_D...12.nex (116.2 Mb)
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Title Kawahara_Breinholt_2014_46taxa_2696loci_Degen_nt12.model.txt
Downloaded 20 times
Description 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.
Download Kawahara_Breinholt_2014_46taxa_2696loci_D...el.txt (43 bytes)
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Title Kawahara_Breinholt_2014_46taxa_2696loci_aa.nex
Downloaded 15 times
Description 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).
Download Kawahara_Breinholt_2014_46taxa_2696loci_aa.nex (58.19 Mb)
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When using this data, please cite the original publication:

Kawahara AY, Breinholt JW (2014) Phylogenomics provides strong evidence for the relationships of butterflies and moths. Proceedings of the Royal Society B 281(1788): 20140970. http://dx.doi.org/10.1098/rspb.2014.0970

Additionally, please cite the Dryad data package:

Kawahara AY, Breinholt JW (2014) Data from: Phylogenomics provides strong evidence for the relationships of butterflies and moths. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.qd27g
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