cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4118/flossmole.sourceforge.2006-04.74
title: sfProjectDesc02-Apr-2006.csv.bz2

description: Project descriptive data.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfProjectDesc02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/500.
DOI: 10.4118/flossmole.sourceforge.2006-04.75
title: sfProjectInfo02-Apr-2006.csv.bz2

description: Project information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfProjectInfo02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/501.
DOI: 10.4118/flossmole.sourceforge.2006-04.76
title: sfProjectList02-Apr-2006.txt.bz2

description: Project list for the source repository.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfProjectList02-Apr-2006.txt.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/502.
DOI: 10.4118/flossmole.sourceforge.2006-04.77
title: sfRawDbEnvData02-Apr-2006.csv.bz2

description: Database environment information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawDbEnvData02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/503.
DOI: 10.4118/flossmole.sourceforge.2006-04.78
title: sfRawDonorData02-Apr-2006.csv.bz2

description: Donor information for projects.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawDonorData02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/504.
DOI: 10.4118/flossmole.sourceforge.2006-04.79
title: sfRawIntAudData02-Apr-2006.csv.bz2

description: Intended audience for the product.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawIntAudData02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/505.
DOI: 10.4118/flossmole.sourceforge.2006-04.80
title: sfRawLicenseData02-Apr-2006.csv.bz2

description: Project license information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawLicenseData02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/506.
DOI: 10.4118/flossmole.sourceforge.2006-04.81
title: sfRawOpSysData02-Apr-2006.csv.bz2

description: Operating system information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawOpSysData02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/507.
DOI: 10.4118/flossmole.sourceforge.2006-04.82
title: sfRawProgLangData02-Apr-2006.csv.bz2

description: Project programming languages.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawProgLangData02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/508.
DOI: 10.4118/flossmole.sourceforge.2006-04.83
title: sfRawStatusData02-Apr-2006.csv.bz2

description: Project status data.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawStatusData02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/509.
DOI: 10.4118/flossmole.sourceforge.2006-04.84
title: sfRawTopicData02-Apr-2006.csv.bz2

description: Project topic information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawTopicData02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/510.
DOI: 10.4118/flossmole.sourceforge.2006-04.85
title: sfRawUserIntData02-Apr-2006.csv.bz2

description: User interface information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawUserIntData02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/511.
DOI: 10.4118/flossmole.sourceforge.2006-04.86
title: sfRawDevProjectData02-Apr-2006.csv.bz2

description: Developers and projects association data.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawDevProjectData02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/512.
DOI: 10.4118/flossmole.sourceforge.2006-04.87
title: sfRawDeveloperData02-Apr-2006.csv.bz2

description: Project developers.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawDeveloperData02-Apr-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/513.
DOI: 10.4118/flossmole.sourceforge.2006-06.100
title: sfRawDbEnvData01-Jun-2006.csv.bz2

description: Database environment information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawDbEnvData01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/526.
DOI: 10.4118/flossmole.sourceforge.2006-06.101
title: sfRawDonorData01-Jun-2006.csv.bz2

description: Donor information for projects.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawDonorData01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/527.
DOI: 10.4118/flossmole.sourceforge.2006-06.102
title: sfRawIntAudData01-Jun-2006.csv.bz2

description: Intended audience for the product.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawIntAudData01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/528.
DOI: 10.4118/flossmole.sourceforge.2006-06.103
title: sfRawLicenseData01-Jun-2006.csv.bz2

description: Project license information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawLicenseData01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/529.
DOI: 10.4118/flossmole.sourceforge.2006-06.104
title: sfRawOpSysData01-Jun-2006.csv.bz2

description: Operating system information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawOpSysData01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/530.
DOI: 10.4118/flossmole.sourceforge.2006-06.105
title: sfRawProgLangData01-Jun-2006.csv.bz2

description: Project programming languages.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawProgLangData01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/531.
DOI: 10.4118/flossmole.sourceforge.2006-06.106
title: sfRawStatusData01-Jun-2006.csv.bz2

description: Project status data.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawStatusData01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/532.
DOI: 10.4118/flossmole.sourceforge.2006-06.107
title: sfRawTopicData01-Jun-2006.csv.bz2

description: Project topic information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawTopicData01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/533.
DOI: 10.4118/flossmole.sourceforge.2006-06.108
title: sfRawUserIntData01-Jun-2006.csv.bz2

description: User interface information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawUserIntData01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/534.
DOI: 10.4118/flossmole.sourceforge.2006-06.95
title: sfProjectDesc01-Jun-2006.csv.bz2

description: Project descriptive data.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfProjectDesc01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/521.
DOI: 10.4118/flossmole.sourceforge.2006-06.96
title: sfProjectInfo01-Jun-2006.csv.bz2

description: Project information.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfProjectInfo01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/522.
DOI: 10.4118/flossmole.sourceforge.2006-06.97
title: sfProjectList01-Jun-2006.csv.bz2

description: Project list for the source repository.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfProjectList01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/523.
DOI: 10.4118/flossmole.sourceforge.2006-06.98
title: sfRawDevProjectData01-Jun-2006.csv.bz2

description: Developers and projects association data.  A .bz2 file of archive/secondary data available as a download from http://downloads.sourceforge.net/ossmole/sfRawDevProjectData01-Jun-2006.csv.bz2. Data collected from SourceForge as raw HTML and parsed into data files by FLOSSmole. Metadata record available at http://flosspapers.org/524.
DOI: 10.5061/dryad.nh1r171j/1
title: Astragalus scaphoides fates
DOI: 10.5061/dryad.nh1r171j/2
title: Astragalus scaphoides fruits.
DOI: 10.5061/dryad.rg148qj4/1
title: Gibsonetal_Evolution_11-0823.R1_DataArchive
DOI: 10.5061/dryad.bj1514fn/1
title: Online Appendix

description: sample information
DOI: 10.5061/dryad.j611s56r/1
title: species_trees

description: 10 species trees used in data simulation
DOI: 10.5061/dryad.j611s56r/2
title: Lanier&Knowles_supplementaryMaterial2

description: Supplementary online figure demonstrating the robustness of STEM to the presence of recombination in a dataset
DOI: 10.5061/dryad.64dv0tg1/2
title: primate-probes-matches.sqlite

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.
DOI: 10.5061/dryad.64dv0tg1/3
title: all-probes

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).
DOI: 10.5061/dryad.64dv0tg1/4
title: probe-matches-to-taxa.sqlite

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).
DOI: 10.5061/dryad.bj1514fn/2
title: suppl Fig 1-6

description: MtDNA based phylogenetic reonstruction for each genus hypothesized from Bayesian analysis. Supports are indicated as follows: Bayesian analysis posterior probabilies*100 and maximum parsimony bootstap values in %. Lineage locations are coded as follows FG=French Guiana, AP=Amapá, SUR=Suriname, GUY=Guyana, PA=Parà, AM=Amazonas, MT=Mato Grosso, N=North, W=West, E=East, S=South, Cr=Center. The bolded area names indicate localities outside the GS.
DOI: 10.5061/dryad.bj1514fn/3
title: suppl Fig 7-12

description: MtDNA based haplotype statistical parsimony networks for each species.
DOI: 10.5061/dryad.bj1514fn/4
title: suppl Fig 13-18

description: Distribution maps for each species indicating major lineages and total range from IUCN database. We also indicated the range of related species in some case for taxonomical considerations.
DOI: 10.5061/dryad.bj1514fn/5
title: suppl Fig 19-24

description: NuDNA based alleles statistical parsimony networks for each species. Colours correspond to the mtDNA major lineages.
DOI: 10.5061/dryad.bj1514fn/7
title: nuDNA datasets
DOI: 10.5061/dryad.64dv0tg1/10
title: birds-uce-anchored-alignments.nexus.tar.bz2

description: BZIP2 archive of NEXUS-formatted file alignments generated, on a locus-by-locus basis, from FASTA sequences in birds-uce-anchored-loci.
DOI: 10.5061/dryad.64dv0tg1/11
title: dbSNP132-to-hg19-uce-200

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.
DOI: 10.5061/dryad.64dv0tg1/12
title: probe-matches-to-taxa.lastz.tar.bz2

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.
DOI: 10.5061/dryad.64dv0tg1/13
title: primate-probes-matches.lastz.tar.bz2

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
DOI: 10.5061/dryad.64dv0tg1/5
title: primate-uce-anchored-loci.fasta.tar.bz2

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.
DOI: 10.5061/dryad.64dv0tg1/6
title: primate-uce-anchored-alignments.nexus.tar.bz2

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.
DOI: 10.5061/dryad.64dv0tg1/7
title: birds-contigs-assembled-from-captures.tar.bz2

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.
DOI: 10.5061/dryad.64dv0tg1/8
title: birds-probe-matches.sqlite

description: SQLITE database of contigs (in birds-contigs-assembled-from-captures.tar.bz2), that match, without duplication, probes within all-probes.fasta.
DOI: 10.5061/dryad.64dv0tg1/9
title: birds-uce-anchored-loci.fasta.bz2

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.
DOI: 10.5061/dryad.64dv0tg1/14
title: birds-probes-matches.lastz.tar.bz2

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.
DOI: 10.5061/dryad.64dv0tg1/15
title: probe-subset-2560-synthesized

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.
DOI: 10.5061/dryad.64dv0tg1/16
title: all-sample-sim1000.txt

description: Simulations results used in Supplementary table indicating the effects of adding additional taxa on the reduction of loci in a complete data matrix.
DOI: 10.5061/dryad.64dv0tg1/17
title: all-sample-sim1000.txt

description: Data used to create Supplementary Figure 7.
DOI: 10.5061/dryad.64dv0tg1/18
title: birds-contig-lengths-by-probe-filtered-birds.csv

description: Data used in Supplementary Figure 1.
DOI: 10.5061/dryad.64dv0tg1/19
title: birds-gc-length-species-matches.csv

description: Data used in Supplementary Figures 2-5.
DOI: 10.5061/dryad.64dv0tg1/20
title: supplementary-tables-and-figures

description: Supplementary Tables 1-4 and Supplementary Figures 1-8.
DOI: 10.5061/dryad.64dv0tg1/21
title: computer-code-README

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.
DOI: 10.7284/138179
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KM2008 using a Hawaii UHDAS instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/138187
title: Anemometer data collected during research cruise KM2008 using a RM Young 85106 instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/138188
title: Anemometer data collected during research cruise KM2008 using a RM Young 85106 instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/138186
title: Barometer data collected during research cruise KM2008 using a Vaisala PTB220 instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/138190
title: Fluorometer data collected during research cruise KM2008 using a WET Labs WETStar instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/138189
title: Gravimeter data collected during research cruise KM2008 using a Bell BGM-3 instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/138191
title: Gyrocompass data collected during research cruise KM2008 using a Sperry NAVIGAT X MK 1 instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/138192
title: INS (Inertial Navigation System) data collected during research cruise KM2008 using a Applanix POS/MV-320 V4 instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/138181
title: Meteorological Station data collected during research cruise KM2008 using a Hawaii MET-System instrument system onboard the platform RV Kilo Moana

description: Processed data created by vessel technician during a Field_expedition
DOI: 10.7284/138194
title: Meteorological Station data collected during research cruise KM2008 using a Hawaii MET-System instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/138182
title: pCO2 (Partial Pressure of Carbon Dioxide) data collected during research cruise KM2008 using a General Oceanics 8050 instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/138195
title: SSV (Sound Speed Velocimeter) data collected during research cruise KM2008 using a AML SV&P instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/138197
title: TSG (Thermosalinograph) data collected during research cruise KM2008 using a Sea-Bird SBE-45 instrument system onboard the platform RV Kilo Moana

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7925/drs1.ucdlib_36571
title: Brigade roll of Roman Catholics

description: Handwritten Brigade Roll, mainly of Roman Catholic members of the 2nd Brigade, 1st Division, British Expeditionary Forces, France.
description: Scope and content: 5 pages have been torn from the notebook.
description: Scope and content: 86 blank pages were checked and certified as blank and were therefore not scanned.
DOI: 10.7925/drs1.ucdlib_36572
title: Diary of Fr. Francis A. Gleeson 23 December 1914 - 29 January 1915

description: Handwritten diary of events of World War I, written while Gleeson was based at Bethune, France. It contains details of his ministry, as well as details of military events and life at the Front.
description: Annotations/handwriting: Parts of the text have been censored by crossing out the writing by hand.
DOI: 10.7925/drs1.ucdlib_36573
title: Brigade roll of mainly Roman Catholics and diary of Fr. Francis A. Gleeson 31 January 1915 - 30 April 1915

description: Handwritten Brigade Roll, mainly of Roman Catholics, fighting with the British Expeditionary Forces, France. It gives names and company details. Also contains some diary entries dated from January to April 1915.
description: Annotations/handwriting: Parts of the text have been censored by crossing out the writing by hand. The direction of the text changes from page 67 on.
description: Scope and content: A number of pages have been completely torn out of the notebook. Pages 9, 11, 17 are partially torn.
description: Scope and content: A number of blank pages were checked and certified as blank and were therefore not scanned.
DOI: 10.7925/drs1.ucdlib_36574
title: Diary of Fr. Francis A. Gleeson 17 January 1915 - 4 October 1915

description: Handwritten dairy with details and military campaigns, life at the Front, deaths of soldiers.
description: Scope and content: 14 blank pages were checked and certified as blank and were therefore not scanned.
DOI: 10.7925/drs1.ucdlib_36575
title: Diary of Fr. Francis A. Gleeson 7 February 1915 - 3 May 1915

description: Handwritten diary with details of life at the Front, military campaigns, soldiers Fr. Gleeson met and much more. Newspaper cutting in diary regarding activities in Neuve Chapelle.
description: Annotations/handwriting: Parts of the text have been censored by crossing out the writing by hand.
description: Scope and content: A number of pages have been completely torn out of the notebook. One leaf is partially torn.
description: Scope and content: Includes a newspaper clipping about Neuve Chapelle.