Data from: Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus)

Perry T, van Loenen AL, Heiniger H, Lee C, Gongora L, Cooper A, Mitchell KJ

Date Published: May 5, 2017

DOI: http://dx.doi.org/10.5061/dryad.71tv1

 

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Title BEAST_files
Downloaded 11 times
Description BEAST files, including input .xml and final maximum clade credibility tree.
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Title RAxML_files
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Description RAxML files, including input alignment & partition file and final tree
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Title PartitionFinder_files
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Description Input & output from PartitionFinder analyses.
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Title 12Files_Platygonus_compressus_SeqData_Filtered_Collapsed.fastq
Downloaded 7 times
Description FASTQ files containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the 12 Platygonus compressus enriched genomic libraries. See main publication for full details on data processing.
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Title 3Files_Pecari_tajacu_SeqData_Filtered_Collapsed.fastq
Downloaded 7 times
Description FASTQ files containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the 3 Pecari tajacu enriched genomic libraries. See main publication for full details on data processing.
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Title Catagonus_wagneri_KY987545_SeqData_Filtered_Collapsed.fastq
Downloaded 4 times
Description FASTQ file containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the Catagonus wagneri enriched genomic library. See main publication for full details on data processing.
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Title Tayassu_pecari_KY987556_SeqData_Filtered_Collapsed.fastq
Downloaded 6 times
Description FASTQ file containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the Tayassu pecari enriched genomic library. See main publication for full details on data processing.
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Title HTS_pipeline_scripts
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Description Scripts for analysis of high-throughput sequencing data.
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Title Consensus sequence from sample ACAD2865
Downloaded 9 times
Description Consensus sequence generated in Geneious. Final sequence too fragmentary for upload to GenBank due to poor DNA preservation. This sequence was excluded from most analyses.
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When using this data, please cite the original publication:

Perry T, van Loenen AL, Heiniger H, Lee C, Gongora L, Cooper A, Mitchell KJ (2017) Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus). Molecular Phylogenetics and Evolution 112: 258-267. http://dx.doi.org/10.1016/j.ympev.2017.03.024

Additionally, please cite the Dryad data package:

Perry T, van Loenen AL, Heiniger H, Lee C, Gongora L, Cooper A, Mitchell KJ (2017) Data from: Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.71tv1
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