Data from: Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes

Sanders JG, Powell S, Kronaue DJC, Vasconcelos HL, Fredrickson ME, Pierce NE

Date Published: December 10, 2013

DOI: http://dx.doi.org/10.5061/dryad.023s6

 

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Title Dryad_Sanders_etal_MolEcol_2013
Downloaded 61 times
Description DIRECTORY: ./example_scripts These are generalized example scripts that should help you to recreate theses analyses using your own data. They are just guides, and will not run without some (limited) modification. There are four files. 1) ./example_scripts/final_parameters.txt QIIME parameters file 2) ./example_scripts/qiime_script_example.sh bash shell script for Qiime 1.4.0 analysis pipeline 3) ./example_scripts/bdiv_summary_example.sh bash shell script for summarizing jacknifed beta diversity results using the QIIME tree_compare.py script. 4) ./example_scripts/bdiv_rugs.py simple python script for creating SVG images to visualize the results from the beta diversity sensitivity analysis performed in (3) above.
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Title figures
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Description DIRECTORY: ./figures This directory contains R code used to generate the alpha rarefaction curves (./figures/alpha), beta diversity box plot comparisons (./figures/box_plots), mantel tests (./figures/mantel), and principle coordinate plots (./figures/PCoA) used in the paper.
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Title ochman_original_data
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Description DIRECTORY: ./ochman_original_data ./ochman_original_data contains the original sequence data as supplied by Prof. Howard Ochman (Personal Communication, July 12, 2013). This is in the format of a combined fasta file (primer_trimed.fasta) and a sample mapping file (sample_map.txt). Additionally, the folder contains a simple python script used to convert the sequence file to Qiime post-split_libraries.py format; the result of this script is ./ochman_example_analysis/seqs.fna.
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Title ochman_example_analysis
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Description DIRECTORY: ./ochman_example_analysis This contains example scripts and analysis similar to the Cephalotes example above. In addition to example output for four OTU widths (./ochman_example_analysis/93, 95, 97, 99), example scripts for analysis at two levels of rarefaction (1000 and 15000 sequences/sample), metadata mapping (./ochman_example_analysis/ochman_split_map.txt), results from the beta diversity sensitivity analysis (./ochman_example_analysis/bdiv_sensitivity_grids), and example host trees (./ochman_example_analysis/ape_phylogram_ILS_relabeled_furcated.tre, ape_cladogram_relabeled_relabeled_furcated.tre), there are several additional files. ape_sample_locations.txt are Lat/Lon values estimated from Figure 1 of Ochman et al 2010, used to estimate geographic distances for the partial Mantel tests.
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Title cephalotes_example_analysis
Downloaded 95 times
Description DIRECTORY: ./cephalotes_example_analysis This contains the denoised sequence data used in the analysis of Cephalotes ant gut microbiota (./cephalotes_example_analysis/seqs.fna), metadata mapping info (cephalotes_map.txt), host trees with individual samples (ceph_guide_tree.tre) and colonies (ceph_species_tree_SpeciesColony.tre) as leaves, and an example analysis script (cephalotes_script_example). It also contains example output from four different OTU clustering thresholds (./cephalotes_example_analysis/93, 95, 97, and 99), results from the beta diversity sensitivity analysis (./cephalotes_example_analysis/bdiv_sensitivity_grids), and the results of the compute_core_microbiome.py script in Qiime 1.6.0 (./cephalotes_example_analysis/core_otus).
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Download README.txt (3.864 Kb)
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When using this data, please cite the original publication:

Sanders JG, Powell S, Kronaue DJC, Vasconcelos HL, Fredrickson ME, Pierce NE (2014) Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes. Molecular Ecology 23(6): 1268–1283. http://dx.doi.org/10.1111/mec.12611

Additionally, please cite the Dryad data package:

Sanders JG, Powell S, Kronaue DJC, Vasconcelos HL, Fredrickson ME, Pierce NE (2014) Data from: Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.023s6
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