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CC BY (54)
Choi, Sang Hyun; Rao, Vikyath D.; Gernat, Tim; Hamilton, Adam R.; Robinson, Gene E.; Goldenfeld, Nigel (2019): Honeybee F2F event data for The origin of heavy tails in honeybee and human interaction times. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4021786_V1
Dataset for F2F events of honeybees. F2F events are defined as face-to-face encounters of two honeybees that are close in distance and facing each other but not connected by the proboscis, thus not engaging in trophallaxis. The first and the second columns show the unique id's of honeybees participating in F2F events. The third column shows the time at which the F2F event started while the fourth column shows the time at which it ended. Each time is in the Unix epoch timestamp in milliseconds.
Rapti, Zoi (2019): Control of bacterial infections via antibiotic-induced proviruses . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9721455_V1
Software (Matlab .m files) for the article: Lying in Wait: Modeling the Control of Bacterial Infections via Antibiotic-Induced Proviruses. The files can be used to reproduce the analysis and figures in the article.
Matlab codes; antibiotic-induced dynamics
Fraebel, David T.; Kuehn, Seppe (2019): Sequencing data for migration rate selection experiments (0.2% agar, 1mM sugar). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2128477_V1
BAM files for evolved strains from migration rate selection experiments conducted in low viscosity (0.2% w/v) agar plates containing M63 minimal medium with 1mM of mannose, melibiose, N-acetylglucosamine or galactose
Yang, Ning; Gao, Jiarong; Lewis, Fred; Yau, Peter; Collins, James; Sweedler, Jonathan; Newmark, Phillip (2019): Data for A novel rotifer derived alkaloid paralyzes schistosome larvae and prevents infection. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1599850_V1
The data set here include data from NMR, LC-MS/MS, MALDI-MS, H/D exchange MS experiments used in paper "A novel rotifer derived alkaloid paralyzes schistosome larvae and prevents infection".
de Moya, Robert (2019): Bemisia tabaci ortholog set. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5333299_V1
This is the published ortholog set derived from whole genome data used for the analysis of members of the B. tabaci complex of whiteflies. It includes the concatenated alignment and individual gene alignments used for analyses (Link to publication: https://www.mdpi.com/1424-2818/11/9/151).
Sashittal, Palash; El-Kebir, Mohammed (2019): SharpTNI Results. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9734610_V1
Results generated using SharpTNI on data collected from the 2014 Ebola outbreak in Sierra Leone.
Christensen, Sarah; Molloy, Erin K.; Vachaspati, Pranjal; Warnow, Tandy (2019): Data from TRACTION: Fast non-parametric improvement of estimated gene trees. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1747658_V1
Datasets used in the study, "TRACTION: Fast non-parametric improvement of estimated gene trees," accepted at the Workshop on Algorithms in Bioinformatics (WABI) 2019.
Gene tree correction; horizontal gene transfer; incomplete lineage sorting
Smith, Rebecca (2019): Mastitis risk effect on the economic consequences of paratuberculosis control in dairy cattle: A stochastic modeling study. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7539223_V1
Simulation data related to the paper "Mastitis risk effect on the economic consequences of paratuberculosis control in dairy cattle: A stochastic modeling study"
Nowak, Jennifer E.; Sweet, Andrew D.; Weckstein, Jason D.; Johnson, Kevin P. (2019): Data for: A molecular phylogenetic analysis of the genera of fruit doves and their allies using dense taxonomic sampling. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9797270_V1
Multiple sequence alignments from concatenated nuclear and mitochondrial genes and resulting phylogenetic tree files of fruit doves and their close relatives. Files include: BEAST input XML file (fruit_dove_beast_input.xml); a maximum clade credibility tree from a BEAST analysis (fruit_dove_beast_mcc.tre); concatenated multiple sequence alignment NEXUS files for the novel dataset (fruit_dove_concatenated_alignment.nex, 76 taxa, 4,277 characters) and the dataset with additional sequences (fruit_dove_plus_cibois_data_concatenated_alignment.nex, 204 taxa, 4,277 characters), both of which contain a MrBayes block including partition information; and 50% majority-rule consensus trees generated from MrBayes analyses, using the NEXUS alignment files as inputs (fruit_dove_mrbayes_consensus.tre, fruit_dove_plus_cibois_data_mrbayes_consensus.tre).
fruit doves; multiple sequence alignment; phylogeny; Aves: Columbidae
Allen, Maximilian (2019): Wisconsin Bobcat Harvest Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2501832_V1
This dataset includes the data from an analysis of bobcat harvest data with particular focus on the relationship between catch-per-unit-effort and population size. The data relate to bobcat trapper and hunter harvest metrics from Wisconsin and include two RDS files which can be open in the software R using the readRDS() function.
bobcat; catch-per-unit-effort; CPUE; harvest; Lynx rufus; wildlife management; trapper; hunter
Skinner, Rachel; Dietrich, Christopher; Walden, Kimberly; Gordon, Eric; Sweet, Andrew; Podsiadlowski, Lars; Petersen, Malte; Simon, Chris; Takiya, Daniela; Johnson, Kevin (2019): Data for Phylogenomics of Auchenorrhyncha (Insecta: Hemiptera) using Transcriptomes: Examining Controversial Relationships via Degeneracy Coding and Interrogation of Gene Conflict. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1461292_V1
The data in this directory corresponds to: Skinner, R.K., Dietrich, C.H., Walden, K.K.O., Gordon, E., Sweet, A.D., Podsiadlowski, L., Petersen, M., Simon, C., Takiya, D.M., and Johnson, K.P. Phylogenomics of Auchenorrhyncha (Insecta: Hemiptera) using Transcriptomes: Examining Controversial Relationships via Degeneracy Coding and Interrogation of Gene Conflict. Systematic Entomology. Correspondance should be directed to: Rachel K. Skinner, firstname.lastname@example.org If you use these data, please cite our paper in Systematic Entomology. The following files can be found in this dataset: Amino_acid_concatenated_alignment.phy: the amino acid alignment used in this analysis in phylip format. Amino_acid_raxml_partitions.txt (for reference only): the partitions for the amino acid alignment, but a partitioned amino acid analysis was not performed in this study. Amino_acid_concatenated_tree.newick: the best maximum likelihood tree with bootstrap values in newick format. ASTRAL_input_gene_trees.tre: the concatenated gene tree input file for ASTRAL README_pie_charts.md: explains the the scripts and data needed to recreate the pie charts figure from our paper. There is also another Corresponds to the following files: ASTRAL_species_tree_EN_only.newick: the species tree with only effective number (EN) annotation ASTRAL_species_tree_pp1_only.newick: the species tree with only the posterior probability 1 (main topology) annotation ASTRAL_species_tree_q1_only.newick: the species tree with only the quartet scores for the main topology (q1) ASTRAL_species_tree_q2_only.newick: the species tree with only the quartet scores for the first alternative topology (q2) ASTRAL_species_tree_q3_only.newick: the species tree with only the quartet scores for the second alternative topology (q3) print_node_key_files.py: script needed to create the following files: node_keys.key: text file with node IDs and topologies complete_q_scores.key: text file with node IDs multiplied q scores EN_node_vals.key: text file with node IDs and EN values create_pie_charts_tree.py: script needed to visualize the tree with pie charts, pp1, and EN values plotted at nodes ASTRAL_species_tree_full_annotation.newick: the species tree with full annotation from the ASTRAL analysis. NOTE: It may be more useful to examine individual value files if you want to visualize the tree, e.g., in figtree, since the full annotations are extensive and can make viewing difficult. Complete_NT_concatenated_alignment.phy: the nucleotide alignment that includes unmodified third codon positions. The alignment is in phylip format. Complete_NT_raxml_partitions.txt: the raxml-style partition file of the nucleotide partitions Complete_NT_concatenated_tree.newick: the best maximum likelihood tree from the concatenated complete analysis NT with bootstrap values in newick format Complete_NT_partitioned_tree.newick: the best maximum likelihood tree from the partitioned complete NT analysis with bootstrap values in newick format Degeneracy_coded_nt_concatenated_alignment.phy: the degeneracy coded nucleotide alignment in phylip format Degeneracy_coded_nt_raxml_partitions.txt: the raxml-style partition file for the degeneracy coded nucleotide alignment Degeneracy_coded_nt_concatenated_tree.newick: the best maximum likelihood tree from the degeneracy-coded concatenated analysis with bootstrap values in newick format Degeneracy_coded_nt_partitioned_tree.newick: the best maximum likelihood tree from the degeneracy-coded partitioned analysis with bootstrap values in newick format count_ingroup_taxa.py: script that counts the number of ingroup and/or outgroup taxa present in an alignment
Auchenorrhyncha; Hemiptera; alignment; trees
Clark, Lindsay V.; Dwiyanti, Maria Stefanie; Anzoua, Kossonou G.; Brummer, Joe E.; Glowacka, Katarzyna; Hall, Megan; Heo, Kweon; Jin, Xiaoli; Lipka, Alexander E.; Peng, Junhua; Yamada, Toshihiko; Yoo, Ji Hye; Yu, Chang Yeon; Zhao, Hua; Long, Stephen P.; Sacks, Erik J. (2019): RAD-seq genotypes for a Miscanthus sinensis diversity panel. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1402948_V1
Genotype calls are provided for a collection of 583 Miscanthus sinensis clones across 1,108,836 loci mapped to version 7 of the Miscanthus sinensis reference genome. Sequence and alignment information for all unique RAD tags is also provided to facilitate cross-referencing to other genomes.
variant call format (VCF); sequence alignment/map format (SAM); miscanthus; single nucleotide polymorphism (SNP); restriction site-associated DNA sequencing (RAD-seq); bioenergy; grass
Buckles, Brittany J; Harmon-Threatt, Alexandra (2019): Data files for "Bee diversity in tallgrass prairies affected by management and its effects on above‐ and below‐ground resources". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0016089_V2
Data used in paper published in the Journal of Applied Ecology titled " Bee diversity in tallgrass prairies affected by management and its effects on above- and below-ground resources" Bee Community file contains info on bees sampled in each site. The first column contain the Tallgrass Prairie Sites sampled all additional columns contain the bee species name in the first row and all individuals recorded. Plant Community file contains info on plants sampled in each site. The first column contain the Tallgrass Prairie Sites sampled all additional columns contain the plant species name in the first row and all individuals recorded. Soil PC1 file contains the soil PC1 values used in the analyses. The first column contain the Tallgrass Prairie Sites sampled, the second column contains the calculated soil PC1 values.
bee; community; tallgrass prairie; grazing
Daniels, Melissa; Larson, Eric (2019): Data for "Effects of forest windstorm disturbance on invasive plants in protected areas of southern Illinois, USA". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1401121_V1
We studied the effect of windstorm disturbance on forest invasive plants in southern Illinois. This data includes raw data on plant abundance at survey points, compiled data used in statistical analyses, and spatial data for surveyed plots and units. This file package also includes a readme.doc file that describes the data in detail, including attribute descriptions.
tornado, blowdowns, derecho, invasive plants, Shawnee National Forest, southern Illinois
MacDonald, Sean; Ward, Michael; Sperry, Jinelle (2019): Manipulating social information to promote frugivory by birds on a Hawaiian Island. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9223847_V1
conspecific attraction; fruit-eating bird; Hawaiian flora; playback experiment; seed dispersal; social information; Zosterops japonicas
Krichels, Alexander (2019): Data For: Iron redox reactions can drive microtopographic variation in upland soil carbon dioxide and nitrous oxide emissions. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8512100_V1
These files contain the data presented in the manuscript entitles "Iron redox reactions can drive microtopographic variation in upland soil carbon dioxide and nitrous oxide emissions".
Iron; redox; carbon dioxide; nitrous oxide; chemodenitrification; Feammox; dissimilatory iron reduction; upland soils; flooding; global change
Miller, Andrew; Raudabaugh, Daniel (2019): Supplemental data sets for Raudabaugh et al., Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1530363_V1
The data set contains Supplemental data sets for the Manuscript entitled "Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi." Environmental sampling: Amplification of nuclear DNA regions (ITS1 and ITS2) were completed using the Fluidigm Access Array and the resulting amplicons were sequenced on an Illumina MiSeq v2 platform runs using rapid 2 × 250 nt paired-end reads. Illumina sequencing run amplicons that were size selected into <500nt and >500nt sub-pools, then remixed together <500nt: >500nt by nM concentration in a 1x:3x proportion. All amplification and sequencing steps were performed at the Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign. ITS1 region primers consisted of ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-'3) and ITS2 (5'-GCTGCGTTCTTCATCGATGC-'3). ITS2 region primers consisted of fITS7 (5'-GTGARTCATCGAATCTTTG-'3) and ITS4 (5'-TCCTCCGCTTATTGATATGC-'3). Supplemental files 1 through 5 contain the raw data files. Supplemental 1 is the ITS1 Illumina MiSeq forward reads and Supplemental 2 is the corresponding index files. Supplemental 3 is the ITS2 Illumina MiSeq forward reads and Supplemental 4 is the corresponding index files. Supplemental 5 is the map file needed to process the forward reads and index files in QIIME. Supplemental 6 and 7 contain the resulting QIIME 1.9.1. OTU tables along with UNITE, NCBI, and CONSTAX taxonomic assignments in addition to the representative OTU sequence. Numeric samples within the OTU tables correspond to the following: 1 Brachythecium sp. 2 Usnea cornuta 3 Dicranum sp. 4 Leucodon julaceus 5 Lobaria quercizans 6 Rhizomnium sp. 7 Dicranum sp. 8 Thuidium delicatulum 9 Myelochroa aurulenta 10 Atrichum angustatum 11 Dicranum sp. 12 Hypnum sp. 13 Atrichum angustatum 14 Hypnum sp. 15 Thuidium delicatulum 16 Leucobryum sp. 17 Polytrichum commune 18 Atrichum angustatum 19 Atrichum angustatum 20 Atrichum crispulum 21 Bryaceae 22 Leucobryum sp. 23 Conocephalum conicum 24 Climacium americanum 25 Atrichum angustatum 26 Huperzia serrata 27 Polytrichum commune 28 Diphasiastrum sp. 29 Anomodon attenuatus 30 Bryoandersonia sp. 31 Polytrichum commune 32 Thuidium delicatulum 33 Brachythecium sp. 34 Leucobryum glaucum 35 Bryoandersonia sp. 36 Anomodon attenuatus 37 Pohlia sp. 38 Cinclidium sp. 39 Hylocomium splendens 40 Polytrichum commune 41 negative control 42 Soil 43 Soil 44 Soil 45 Soil 46 Soil 47 Soil If a sample number is not present within the OTU table; either no sequences were obtained or no sequences passed the quality filtering step in QIIME. Supplemental 8 contains the Summary of unique species per location.
Rando, Halie; Wadlington, William; Johnson, Jennifer; Stutchman, Jeremy; Trut, Lyudmila; Farré, Marta; Kukekova, Anna (2019): Red Fox (Vulpes vulpes) Y-Chromosome Sequence. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4447017_V1
This dataset contains raw data associated with the red fox Y-chromosome assembly (see https://doi.org/10.3390/genes10060409). It includes a fasta file of the 171 scaffolds from the red fox reference genome assembly identified as likely to contain Y-chromosome sequence, the raw BLAST results, and the ABySS assemblies described in the manuscript.
Y-chromosome; carnivore; Vulpes vulpes; sex chromosomes; MSY; Y-chromosome genes; copy-number variation; BCORY2; UBE1Y; next-generation sequencing
Krichels, Alexander (2019): Data for: Dynamic controls on field-scale soil nitrous oxide hot spots and hot moments across a microtopographic gradient. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9733959_V1
This dataset includes all data presented in the manuscript entitled: "Dynamic controls on field-scale soil nitrous oxide hot spots and hot moments across a microtopographic gradient"
denitrification; depressions; microtopography; nitrous oxide; soil oxygen; soil temperature
Detmer, Thomas; Wahl, David (2019): Trophic cascade strength is influenced by size frequency distribution of primary consumers and size-selective predation: examined with mesocosms and modeling. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3292716_V1
Data set of trophic cascade in mesocosms experiments for zooplankton (biomass and body size) and phytoplankton (chlorophyll a concentration) caused by Bluegill as well as zooplankton production in those same treatment groups. Zooplankton were collected by tube sampler and phytoplankton were collected through grab samples.
Trophic cascades; size-selective predation; compensatory mechanisms; biomanipulation; invasive fish; Daphnia; Moina
Pradhan, Dikshant; Jensen, Paul (2019): Pradhan 2019 Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3352362_V1
Data necessary for production of figures presented in "Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models" by Pradhan et al.
Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models;
Detmer, Thomas (2019): Influences of fish on food web structure and function in mountain lakes supplemental data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5372808_V1
The associated data sets include information on stable isotopes from organic matter sources in high elevation lakes, the percentage of production assimilated from the different sources of organic matter, and the relationship between different metrics for trophic position and environmental variables.
Stable isotopes; macroinvertebrate production; trophic position
Molloy, Erin K.; Warnow, Tandy (2019): Data from: Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0569467_V2
This repository includes scripts and datasets for the paper, "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge." All data files in this repository are for analyses using the logdet distance matrix computed on the concatenated alignment. Data files for analyses using the average gene-tree internode distance matrix can be downloaded from the Illinois Data Bank (https://doi.org/10.13012/B2IDB-1424746_V1). The latest version of NJMerge can be downloaded from Github (https://github.com/ekmolloy/njmerge).<br /> <strong>List of Changes:</strong> • Updated timings for NJMerge pipelines to include the time required to estimate distance matrices; this impacted files in the following folder: <strong>data.zip</strong> • Replaced "Robinson-Foulds" distance with "Symmetric Difference"; this impacted files in the following folders: <strong> tools.zip; data.zip; scripts.zip</strong> • Added some additional information about the java command used to run ASTRAL-III; this impacted files in the following folders: <strong>data.zip; astral64-trees.tar.gz (new)</strong>
divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics
Molloy, Erin K.; Warnow, Tandy (2018): NJMerge: A generic technique for scaling phylogeny estimation methods and its application to species trees. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1424746_V1
This repository includes scripts, datasets, and supplementary materials for the study, "NJMerge: A generic technique for scaling phylogeny estimation methods and its application to species trees", presented at RECOMB-CG 2018. The supplementary figures and tables referenced in the main paper can be found in njmerge-supplementary-materials.pdf. The latest version of NJMerge can be downloaded from Github: https://github.com/ekmolloy/njmerge. ***When downloading datasets, please note that the following errors.*** In README.txt, lines 37 and 38 should read: + fasttree-exon.tre contains lines 1-25, 1-100, or 1-1000 of fasttree-total.tre + fasttree-intron.tre contains lines 26-50, 101-200, or 1001-2000 of fasttree-total.tre Note that the file names (fasttree-exon.tre and fasttree-intron.tre) are swapped. In tools.zip, the compare_trees.py and the compare_tree_lists.py scripts incorrectly refer to the "symmetric difference error rate" as the "Robinson-Foulds error rate". Because the normalized symmetric difference and the normalized Robinson-Foulds distance are equal for binary trees, this does not impact the species tree error rates reported in the study. This could impact the gene tree error rates reported in the study (see data-gene-trees.csv in data.zip), as FastTree-2 returns trees with polytomies whenever 3 or more sequences in the input alignment are identical. Note that the normalized symmetric difference is always greater than or equal to the normalized Robinson-Foulds distance, so the gene tree error rates reported in the study are more conservative. In njmerge-supplementary-materials.pdf, the alpha parameter shown in Supplementary Table S2 is actually the divisor D, which is used to compute alpha for each gene as follows. 1. For each gene, a random value X between 0 and 1 is drawn from a uniform distribution. 2. Alpha is computed as -log(X) / D, where D is 4.2 for exons, 1.0 for UCEs, and 0.4 for introns (as stated in Table S2). Note that because the mean of the uniform distribution (between 0 and 1) is 0.5, the mean alpha value is -log(0.5) / 4.2 = 0.16 for exons, -log(0.5) / 1.0 = 0.69 for UCEs, and -log(0.5) / 0.4 = 1.73 for introns.
phylogenomics; species trees; incomplete lineage sorting; divide-and-conquer
Molloy, Erin K.; Warnow, Tandy (2019): Data from: TreeMerge: A new method for improving the scalability of species tree estimation methods. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9570561_V1
This repository includes scripts and datasets for the paper, "TreeMerge: A new method for improving the scalability of species tree estimation methods." The latest version of TreeMerge can be downloaded from Github (https://github.com/ekmolloy/treemerge).
divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics