Data from: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT

Date Published: January 30, 2013

DOI: http://dx.doi.org/10.5061/dryad.sd080

 

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Title birds-contigs-assembled-from-uce-loci.fasta.gz
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Description UCE contigs assembled from raw reads collected using target enrichment.
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Title birds-lastz-matches-of-probes-to-contigs.lastz.tar.gz
Downloaded 42 times
Description LASTZ matches of probes to species-specific contigs in contigs-assembled-from-uce-loci.fasta.gz
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Title birds-matches-of-probes-to-contigs.sqlite.gz
Downloaded 32 times
Description SQLITE database of LASTZ matches between assembled contigs in birds-contigs-assembled-from-uce-loci.fasta.gz and the UCE probes. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment. These data are derived from birds-lastz-matches-of-probes-to-contigs.lastz.tar.gz.
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Title birds-416-loci-alignments.tar.gz
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Description Nexus formatted, complete (all taxa have data at all loci) alignments of 416 UCE loci enriched from birds.
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Title birds-416-loci-subs-models.txt
Downloaded 56 times
Description Substitution models estimated for 416 locus data set.
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Title birds-416-loci-mrbayes.gz
Downloaded 67 times
Description Nexus formatted, concatenated alignment of 416 UCE loci enriched from birds.
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Title birds-416-loci-cloudforest-output.tar.gz
Downloaded 43 times
Description Genetrees and boostrap replicates generated from 416 loci using Cloudforest.
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Title birds-1541-loci-alignments.tar.gz
Downloaded 51 times
Description Nexus formatted, complete (all taxa have data at all loci) alignments of 1541 UCE loci enriched from birds.
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Title birds-1541-loci-subs-models
Downloaded 42 times
Description Substitution models estimated for 1541 locus data set.
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Title birds-1541-loci-mrbayes.gz
Downloaded 46 times
Description Nexus formatted, concatenated alignment of 1541 UCE loci enriched from birds.
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Title birds-416-loci-raxml.phylip.gz
Downloaded 30 times
Description Phylip formatted, concatenated alignment of 416 UCE loci enriched from birds.
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Title birds-1541-loci-raxml.phylip.gz
Downloaded 30 times
Description Phylip formatted, concatenated alignment of 1541 UCE loci enriched from birds.
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When using this data, please cite the original publication:

McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT (2013) A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS ONE 8(1): e54848. http://dx.doi.org/10.1371/journal.pone.0054848

Additionally, please cite the Dryad data package:

McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT (2013) Data from: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.sd080
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