Data from: Accounting for uncertainty in gene tree estimation: summary-coalescent species tree inference in a challenging radiation of Australian lizards

Blom MPK, Bragg JG, Potter S, Moritz C

Date Published: September 28, 2016

DOI: http://dx.doi.org/10.5061/dryad.91867

 

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Title concatenated dataset used for RAxML analysis
Downloaded 15 times
Description Concatenated alignment of the complete dataset (1361 loci) and the inferred maximum likelihood RAxML tree (100 tree searches, 1000 bootstrap replicates)
Download RAxML.tar.gz (4.463 Mb)
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Title Alignments
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Description All 1852 loci (contains both complete and incomplete, up to 1 species missing, alignments)
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Title ASTRAL complete dataset, random locus subsets
Downloaded 8 times
Description The ASTRAL input and output for the summary-coalescent species tree analysis based on the complete dataset. Locus subsets were randomly (i.e. not ranked by Tree Certainty score) selected.
Download ASTRAL_0_indiv_miss_allowed_RANDOM.tar.gz (24.43 Mb)
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Title ASTRAL complete dataset, ranked locus subsets
Downloaded 11 times
Description The ASTRAL input and output for the summary-coalescent species tree analysis based on the complete dataset. Locus subsets were ranked (i.e. ranked by Tree Certainty score) selected.
Download ASTRAL_0_indiv_miss_allowed_RANKED.tar.gz (24.41 Mb)
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Title ASTRAL incomplete dataset, random locus subsets
Downloaded 6 times
Description The ASTRAL input and output for the summary-coalescent species tree analysis based on the incomplete dataset. Locus subsets were randomly (i.e. not ranked by Tree Certainty score) selected.
Download ASTRAL_1_indiv_miss_allowed_RANDOM.tar.gz (33.57 Mb)
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Title ASTRAL incomplete dataset, ranked locus subsets
Downloaded 7 times
Description The ASTRAL input and output for the summary-coalescent species tree analysis based on the complete dataset. Locus subsets were ranked (i.e. ranked by Tree Certainty score) selected.
Download ASTRAL_1_indiv_miss_allowed_RANKED.tar.gz (33.56 Mb)
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Title Supplementary_Table_1
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Description Information on individuals used in the study and sequencing success
Download Supplementary_Table_1.doc (40.44 Kb)
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Title Supplementary figures
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Description Supplementary figures in order and as described in manuscript
Download supp_figures_V2.pdf (239.7 Kb)
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When using this data, please cite the original publication:

Blom MPK, Bragg JG, Potter S, Moritz C (2017) Accounting for uncertainty in gene tree estimation: summary-coalescent species tree inference in a challenging radiation of Australian lizards. Systematic Biology 66(3):352-366. http://dx.doi.org/10.1093/sysbio/syw089

Additionally, please cite the Dryad data package:

Blom MPK, Bragg JG, Potter S, Moritz C (2016) Data from: Accounting for uncertainty in gene tree estimation: summary-coalescent species tree inference in a challenging radiation of Australian lizards. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.91867
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