Data from: Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data

 

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Title Breinholt_Kawahara_2013_nuc
Downloaded 15 times
Description Nexus file containing 938 genes for 19 taxa. See Taxon_list.txt for names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene. Gene names correspond to gene numbers in the Insecta HMMER v3-2 core ortholog database. For further information on these genes see Supplementary Table 2 from Breinholt and Kawahara 2013.
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Title Breinholt_Kawahara_2013_aa.nex
Downloaded 10 times
Description Nexus file containing 938 genes for 19 taxa. See taxa_list.txt for names of each taxon, this is a amino acid nexus file with a CHARSET that defines each gene. Gene names correspond to gene numbers in the Insecta HMMER v3-2 core ortholog database. For further information on these genes see Supplementary Table 2 from Breinholt and Kawahara 2013.
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Title Taxon_list.txt
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Description List of taxa codes and names and source of data for the two nexus files below in tab-delimited text.
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Title acti2_assembly.fasta
Downloaded 10 times
Description Assembly of Actias luna from Genbank SRA accession #SRR1002974, 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 SOAP_assembly.qsub for the command used for this assembly.
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Title attac_assembly.fasta
Downloaded 12 times
Description Assembly of Attacus atlas from Genbank SRA accession #SRR1002994, 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 SOAP_assembly.qsub for the command used for this assembly.
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Title cundu3_assembly.fasta
Downloaded 11 times
Description Assembly of Ceratomia undulosa from Genbank SRA accession #SRR1002985, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and process with the fastx toolkit. See SOAP_assembly.qsub for the command used for this assembly.
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Title dara_assembly.fasta
Downloaded 9 times
Description Assembly of Darapsa myron from Genbank SRA accession #SRR1002986, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and process with the fastx toolkit. See SOAP_assembly.qsub for the command used for this assembly.
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Title elug1_assembly.fasta
Downloaded 5 times
Description Assembly of Enyo lugubris from Genbank SRA accession #SRR1002983, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and process with the fastx toolkit. See SOAP_assembly.qsub for the command used for this assembly.
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Title hema2_assembly
Downloaded 7 times
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Title SOAP_assembly.qsub
Downloaded 10 times
Description This script was used for multiple kmer transcriptome assemblies. The script is specific to the University of Florida module system but can be easily edited for use on other HPC systems.
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Title HaMStR.qsub
Downloaded 8 times
Description This script contains commands used for HaMStR ortholog prediction. It is specific to HPC systems with PBS schedulers and requires the set of files and directories detailed in the HaMStR manual.
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Title README.txt
Downloaded 23 times
Description This file contains descriptions of all the files associated with this Dryad package.
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When using this data, please cite the original publication:

Breinholt JW, Kawahara AY (2013) Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data. Genome Biology and Evolution 5(11): 2082-2092. http://dx.doi.org/ 10.1093/gbe/evt157

Additionally, please cite the Dryad data package:

Breinholt JW, Kawahara AY (2013) Data from: Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r5cq0.2
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