Data from: A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)

Faircloth BC, Sorenson L, Santini F, Alfaro ME

Date Published: June 19, 2013

DOI: http://dx.doi.org/10.5061/dryad.j015n

 

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Title fish-500-loci-enrichment-probes.fasta.gz
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Description Fasta file of 120 BP probe sequences commercially synthesized to target UCE loci in ray-finned-fishes.
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Title fish-contigs-from-uce-enrichments.tar.gz
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Description FASTA file of contigs assembled from raw reads generated by sequencing enriched libraries of several reptile species.
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Title fish-lastz-probe-matches-to-uce-contigs.tar.gz
Downloaded 22 times
Description LASTZ matches of probes to species-specific contigs in fish-contigs-from-uce-enrichments.tar.gz
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Title fish-lastz-probe-matches-to-genome-enabled.tar.gz
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Description LASTZ matches of probes to data from genome-enabled fishes.
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Title fish-probe-matches-to-uce-contigs.sqlite.gz
Downloaded 19 times
Description SQLITE database of LASTZ matches (from fish-lastz-probe-matches-to-uce-contigs.tar.gz) between assembled contigs in fish-contigs-from-uce-enrichments.tar.gz and the UCE probes in fish-500-loci-enrichment-probes.fasta.gz. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment.
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Title fish-probe-matches-to-genome-enabled.sqlite.gz
Downloaded 18 times
Description SQLITE database of LASTZ matches between data from genome-enabled taxa and the UCE probes in fish-500-loci-enrichment-probes.fasta.gz. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment.
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Title fish-nexus-files-from-uce-alignment.tar.gz
Downloaded 32 times
Description NEXUS alignment files for all taxa across UCE loci, lacking entries for taxa with missing data.
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Title fish-nexus-files-with-gaps-from-uce-alignment.tar.gz
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Description NEXUS alignment files for all taxa across UCE loci, having entries for taxa with missing data.
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Title fish-nexus-file-for-mrbayes.nexus.gz
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Description NEXUS-formatted alignment file for use with MRBAYES.
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Title fish-phylip-file-for-raxml.phylip.gz
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Description PHYLIP formatted alignment file for use with RAXML.
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Title fish-partitioned-phylip-file-for-raxml-partitions.txt.gz
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Description Partitions for use with RAXML.
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Title fish-partitioned-phylip-file-for-raxml.phylip.gz
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Description Partitioned PHYLIP file for use with RAXML.
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Title fish-phylip-files-for-cloudforest-with-pol_sen-and-aci_ful.tar.gz
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Description PHYLIP-formatted alignment file for use with CLOUDFOREST. Polypterus senegalus and Acipenser fulvescens are present in all alignements. Alignment matrices may be incomplete for other taxa.
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Title fish-genetree-results-from-cloudforest.tre.gz
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Description Gene trees generated by CLOUDFOREST.
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Title fish-genetree-bootrep-results-from-cloudforest.tar.gz
Downloaded 17 times
Description Gene tree bootstrap replicates generated by CLOUDFOREST.
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Title fish-computer-code-README.txt
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Description README file providing details about computer code used as part of this research project.
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When using this data, please cite the original publication:

Faircloth BC, Sorenson L, Santini F, Alfaro ME (2013) A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS ONE 8(6): e65923. http://dx.doi.org/10.1371/journal.pone.0065923

Additionally, please cite the Dryad data package:

Faircloth BC, Sorenson L, Santini F, Alfaro ME (2013) Data from: A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.j015n
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