Data from: Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales

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

Date Published: December 16, 2011

DOI: http://dx.doi.org/10.5061/dryad.64dv0tg1

 

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Title primate-probes-matches.sqlite
Downloaded 113 times
Description SQLITE database of all-probes matches to various primate genome sequences. 'matches' tables shows match status (1 = TRUE) of probes to genomes and 'match-map' shows the primate contig matched and the orientation of the match.
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Title all-probes
Downloaded 158 times
Description FASTA-formatted text file of UCE-anchored probe sequences, designed from UCEs identified across Reptiles (birds and lizard). We (1) aligned these sequences to extant primate genomic sequences and (2) used synthetic oligos identical to a subset of these sequences to enrich target DNA in birds. Fasta header gives probes location relative to chromosomes of galGal3 (UCSC).
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Title probe-matches-to-taxa.sqlite
Downloaded 110 times
Description SQLITE database of all-probes.fasta matches to genome-enabled vertebrate taxa (Supplementary Table 1). Column value of 1 = TRUE (meaning there was a match).
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Title primate-uce-anchored-loci.fasta.tar.bz2
Downloaded 89 times
Description BZIP2 file of FASTA sequences sliced from primate genomes that include the match-site of probes within the all-probes.fasta file ± flanking sequence. The archive contains fasta files for each primate in Supplementary Table 2.
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Title primate-uce-anchored-alignments.nexus.tar.bz2
Downloaded 84 times
Description NEXUS-formatted files providing alignments of UCE-anchored genomic regions identified in primate genomes where probes from all-probes.fasta matches respective primate genomes. We used these alignments to reconstruct the primate phylogeny.
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Title birds-contigs-assembled-from-captures.tar.bz2
Downloaded 92 times
Description BZIP2 archive of FASTA files providing bird contigs assembled from reads following target enrichment with a subset of probes in all-probes.fasta. Archive contains one file per species.
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Title birds-probe-matches.sqlite
Downloaded 114 times
Description SQLITE database of contigs (in birds-contigs-assembled-from-captures.tar.bz2), that match, without duplication, probes within all-probes.fasta.
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Title birds-uce-anchored-loci.fasta.bz2
Downloaded 84 times
Description BZIP2 archive of FASTA files, corresponding to those contigs matching target enrichment probes (in birds-probe-matches.sqlite) that are not duplicated. We assemble these reads, on a locus-by-locus basis to generate the alignments in birds-uce-anchored-alignments.nexus.
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Title birds-uce-anchored-alignments.nexus.tar.bz2
Downloaded 78 times
Description BZIP2 archive of NEXUS-formatted file alignments generated, on a locus-by-locus basis, from FASTA sequences in birds-uce-anchored-loci.
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Title dbSNP132-to-hg19-uce-200
Downloaded 99 times
Description CSV-formatted file giving the UCE overlapping SNP locations present in dbSNP132. The 'snp-name' column gives the rs-accession for the SNP record.
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Title probe-matches-to-taxa.lastz.tar.bz2
Downloaded 57 times
Description TAB-delimited LASTZ output from matches of probes in all-probes.fasta to the vertebrate genomes in Supplementary Table 1. We parsed this file to remove duplicates. We archived results for non-duplicated matches in probe-matches-to-taxa.sqlite.
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Title primate-probes-matches.lastz.tar.bz2
Downloaded 56 times
Description TAB-delimited LASTZ output from matches of probes in all-probes.fasta to the primate genomes in Supplementary Table 2. We parsed this file to remove duplicates. We archived results for non-duplicated matches in primate-probes-matches.sqlite
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Title birds-probes-matches.lastz.tar.bz2
Downloaded 58 times
Description TAB-delimited LASTZ output from matches of probes in all-probes.fasta to the vertebrate genomes in Supplementary Table 3. We parsed this file to remove duplicates. We archived results for non-duplicated matches in birds-probe-matches.sqlite.
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Title probe-subset-2560-synthesized
Downloaded 61 times
Description FASTA file of the subset of 2,560 probes from all-probes that we synthesized for in vitro targeted capture of 2,386 loci in birds. FASTA header gives the probe id, the probe position in the chicken (galGal3) genome, and the count of probes targeting that locus.
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Title all-sample-sim1000.txt
Downloaded 29 times
Description Simulations results used in Supplementary table indicating the effects of adding additional taxa on the reduction of loci in a complete data matrix.
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Title all-sample-sim1000.txt
Downloaded 32 times
Description Data used to create Supplementary Figure 7.
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Title birds-contig-lengths-by-probe-filtered-birds.csv
Downloaded 32 times
Description Data used in Supplementary Figure 1.
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Title birds-gc-length-species-matches.csv
Downloaded 44 times
Description Data used in Supplementary Figures 2-5.
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Title supplementary-tables-and-figures
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Description Supplementary Tables 1-4 and Supplementary Figures 1-8.
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Title computer-code-README
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Description Location, commit (i.e., snapshot), and URL information for computer code used as part of this manuscript. Placed into Dryad in lieu of committing code under CC0.
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When using this data, please cite the original publication:

Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC (2011) Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales. Systematic Biology 61(5): 717-726. http://dx.doi.org/10.1093/sysbio/sys004

Additionally, please cite the Dryad data package:

Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC (2011) Data from: Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.64dv0tg1
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