Data from: Allele phasing greatly improves the phylogenetic utility of ultraconserved elements

Andermann T, Fernandes AM, Olsson U, Töpel M, Pfeil B, Oxelman B, Aleixo A, Faircloth BC, Antonelli A

Date Published: May 14, 2018

DOI: https://doi.org/10.5061/dryad.hq3vq

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Title assembler_test
Downloaded 9 times
Description This zip-archive contains all files related to our testing of different de novo assemblers and their treatment of heterozygous sites. The archive also contains the results of a reference-based assembly of the sequencing reads against reference sequences for all UCE loci.
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Title phylogenetic_analyses
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Description This zip-archive contains all input files and results of the Multispecies Coalescent (MSC) analyses from this study. This includes the BEAST analyses of the mitochondrial genome, the STACEY analyses of all sequence data and the SNAPP analyses of all SNP datasets.
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Title summary_coalescent_analyses
Downloaded 9 times
Description This zip-archive contains all files related to the MPEST analyses, which are reported in online Appendix 2. This includes gene trees for all loci inferred by PhyML and the MPEST species tree analyses results.
Download summary_coalescent_analyses.zip (426.5 Mb)
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Title phasing_files
Downloaded 6 times
Description This zip-archive contains all files related to the reference based assembly of UCE sequencing reads and the subsequent phasing of these reads into allele haplotype sequences.
Download phasing_files.zip (410.3 Mb)
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Title simulations
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Description This zip-archive contains all files related to the simulation of data generated in this study.
Download simulations.zip (91.75 Mb)
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Title alignments
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Description This zip-archive contains all sequence and SNP multiple sequence alignment (MSA) files that were analyzed in this study.
Download alignments.zip (44.87 Mb)
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Title supplemental_material
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Description Zip-archive contains online Appendices 1-5, Supplementary Figs. S1-S11 and Supplementary Tables S1 and S2.
Download supplemental_material.zip (12.50 Mb)
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Title tree_processing
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Description This zip-archive contains all steps that were executed post tree inference, including the extraction and plotting of node-height distributions, the generation of similarity matrices and the calculation of the maximum clade credibility trees for all MSC analyses.
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When using this data, please cite the original publication:

Andermann T, Fernandes AM, Olsson U, Töpel M, Pfeil B, Oxelman B, Aleixo A, Faircloth BC, Antonelli A (2018) Allele phasing greatly improves the phylogenetic utility of ultraconserved elements. Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syy039

Additionally, please cite the Dryad data package:

Andermann T, Fernandes AM, Olsson U, Töpel M, Pfeil B, Oxelman B, Aleixo A, Faircloth BC, Antonelli A (2018) Data from: Allele phasing greatly improves the phylogenetic utility of ultraconserved elements. Dryad Digital Repository. https://doi.org/10.5061/dryad.hq3vq
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