Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation

Pease JB, Haak DC, Hahn MW, Moyle LC

Date Published: March 8, 2016

DOI: https://doi.org/10.5061/dryad.182dv

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Title Combined VCF for all 29 accessions for chromosome 0
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Title Combined VCF for all 29 accessions for chromosome 1
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Download Pease_etal_SL2.50ch01.vcf.gz (716.1 Mb)
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Title Combined VCF for all 29 accessions for chromosome 2
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Download Pease_etal_SL2.50ch02.vcf.gz (492.5 Mb)
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Title Combined VCF for all 29 accessions for chromosome 3
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Download Pease_etal_SL2.50ch03.vcf.gz (537.8 Mb)
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Title Combined VCF for all 29 accessions for chromosome 4
Downloaded 3 times
Download Pease_etal_SL2.50ch04.vcf.gz (479.0 Mb)
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Title Combined VCF for all 29 accessions for chromosome 5
Downloaded 3 times
Download Pease_etal_SL2.50ch05.vcf.gz (428.4 Mb)
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Title Combined VCF for all 29 accessions for chromosome 6
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Download Pease_etal_SL2.50ch06.vcf.gz (421.0 Mb)
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Title Combined VCF for all 29 accessions for chromosome 7
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Download Pease_etal_SL2.50ch07.vcf.gz (448.8 Mb)
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Title Combined VCF for all 29 accessions for chromosome 8
Downloaded 2 times
Download Pease_etal_SL2.50ch08.vcf.gz (434.7 Mb)
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Title Combined VCF for all 29 accessions for chromosome 9
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Download Pease_etal_SL2.50ch09.vcf.gz (451.3 Mb)
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Title Combined VCF for all 29 accessions for chromosome 10
Downloaded 4 times
Download Pease_etal_SL2.50ch10.vcf.gz (421.6 Mb)
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Title Combined VCF for all 29 accessions for chromosome 11
Downloaded 2 times
Download Pease_etal_SL2.50ch11.vcf.gz (392.2 Mb)
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Title Combined VCF for all 29 accessions for chromosome 12
Downloaded 4 times
Download Pease_etal_SL2.50ch12.vcf.gz (420.7 Mb)
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Title Raw Reads located at NCBI BioProject PRJNA305880
Description http://www.ncbi.nlm.nih.gov/bioproject/305880
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Title HQ Alignment in Multisample Variant Format
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Download Pease_etal_Tomato29acc_HQ.mvf.gz (594.3 Mb)
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Title HD Alignment in Multisample Variant Format
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Download Pease_etal_Tomato29acc_HD.mvf.gz (604.6 Mb)
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Title LQ Alignment in Multisample Variant Format
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Download Pease_etal_Tomato29acc_LQ.mvf.gz (633.0 Mb)
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Title HQ Coding Sequence Alignment in Multisample Variant Format
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Download Pease_etal_Tomato29acc_HQ_prot.mvf.gz (113.6 Mb)
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Title Genome-wide all sample phylogenies from gene regions, 100kb and 1Mb regions
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Download Pease_etal_TomatoPhylo_GeneTrees.tar.gz (5.449 Mb)
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Title Genome-Wide Concatenated/Coalescent/Consensus Phylogenies
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Download Pease_etal_TomatoPhylo_GenomeWideTrees.tar.gz (129.3 Kb)
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Title Quartet Gene Trees, D-statistics, and DFOIL results for Figs S4/5
Downloaded 6 times
Download Pease_etal_TomatoPhylo_QuartetTreeDstatsDF...ar.gz (4.529 Mb)
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When using this data, please cite the original publication:

Pease JB, Haak DC, Hahn MW, Moyle LC (2016) Phylogenomics reveals three sources of adaptive variation during a rapid radiation. PLOS Biology 14(2): e1002379. https://doi.org/10.1371/journal.pbio.1002379

Additionally, please cite the Dryad data package:

Pease JB, Haak DC, Hahn MW, Moyle LC (2016) Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation. Dryad Digital Repository. https://doi.org/10.5061/dryad.182dv
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