Data from: The effects of model choice and mitigating bias on the ribosomal tree of life

Lasek-Nesselquist E, Gogarten JP

Date Published: June 13, 2013

DOI: http://dx.doi.org/10.5061/dryad.7785h

 

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Title aeb1 phylogenies
Downloaded 35 times
Description The Aeb1 phylogenies include representatives of all major phyla/supergroups for the three domains of life (when available). Archaea, Eukarya, and Bacteria protein sequences were aligned at once (no profile alignment) and protein alignments were trimmed individually and then concatenated into a supermatrix (resulting in 13432 positions). Aeb1 contains no “Archezoan” sequences (polyphyletic group of long branched eukaryotes such as Giardia, Trichomonas, Microsporidia, and Entamoeba) but has some fast evolving eukaryotes, including Euglenozoa. Methods of inference included maximum likelihood as implemented in RAxML, PhyML-4X (Le et al., 2012), and PhyML-Structure (Le and Gascuel, 2010) or Bayesian inference as implemented in PhyloBayes v. 3.3 or 3.3e (Lartillot et al., 2009).
Download README.txt (399 bytes)
Download aeb1.alltrees.tree (33.27 Kb)
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Title aeb2 phylogenies
Downloaded 29 times
Description Aeb2 includes members of Bacteria, Archaea, and Eukarya. Methods of tree inference included maximum likelihood as implemented in RAxML, PhyML-4X (Le et al., 2012), and PhyML-Structure (Le and Gascuel, 2010) or Bayesian inference as implemented in PhyloBayes v. 3.3 or 3.3e (Lartillot et al., 2009). Aeb2 includes “Archezoan” (polyphyletic group of long branched eukaryotes such as Giardia, Trichomonas, Microsporidia, and Entamoeba) sequences; the subset “aeb2 Arch+” refers to the presence of Archezoa without Korarchaeota and Thaumarchaeota and the subset, “aeb2 KT+” refers to the presence of Korarchaeota and Thaumarchaeota without Archezoa. Aeb2 Arch+ and KT+ attempt to mitigate long-branch attraction (LBA) artifacts due to substitution rate saturation and allow us to assess the influence of taxonomic sampling on phylogenetic outcome. Gap removal occurred after the creation of the supermatrix (resulting in 13929 positions for aeb2 Arch+ and 13941 positions for aeb2 KT+).
Download README.txt (770 bytes)
Download aeb2.alltrees.tree (55.77 Kb)
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Title aeb3 phylogenies
Downloaded 33 times
Description Methods of inference included maximum likelihood as implemented in RAxML, PhyML-4X (Le et al., 2012), and PhyML-Structure (Le and Gascuel, 2010) or Bayesian inference as implemented in PhyloBayes v. 3.3 or 3.3e (Lartillot et al., 2009). Aeb3 comprises representatives from each phylum/supergroup with no sequences from Archezoa or Euglenozoa and trimming performed after the construction of the supermatrix (resulting in 17876 positions). The removal of the fast-evolving Euglenozoa represents an attempt to further mitigate LBA artifacts. To examine the effects of missing data and specifically test how missing data influences the relationship between Archaea and Eukarya, ribosomal proteins shared by Archaea and Eukarya were deleted from some archaeal taxa.
Download README.txt (262 bytes)
Download aeb3.alltrees.tree (14.22 Kb)
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Title aeb1 alignment
Downloaded 19 times
Description aeb1 alignment in fasta format
Download aeb1.fas (1.453 Mb)
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Title aeb2 Arch+ alignment
Downloaded 13 times
Download aeb2_Arch.fas (2.093 Mb)
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Title aeb2 KT+ alignment
Downloaded 12 times
Download aeb2_KT.fas (2.080 Mb)
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Title aeb3 alignment
Downloaded 13 times
Description Aeb3 comprises representatives from each phylum/supergroup with no sequences from Archezoa or Euglenozoa and trimming performed after the construction of the supermatrix (resulting in 17876 positions). The removal of the fast-evolving Euglenozoa represents an attempt to further mitigate LBA artifacts. To examine the effects of missing data and specifically test how missing data influences the relationship between Archaea and Eukarya, ribosomal proteins shared by Archaea and Eukarya were deleted from some archaeal taxa.
Download aeb3.fas (1.038 Mb)
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When using this data, please cite the original publication:

Lasek-Nesselquist E, Gogarten JP (2013) The effects of model choice and mitigating bias on the ribosomal tree of life. Molecular Phylogenetics and Evolution 69(1): 17–38. http://dx.doi.org/10.1016/j.ympev.2013.05.006

Additionally, please cite the Dryad data package:

Lasek-Nesselquist E, Gogarten JP (2013) Data from: The effects of model choice and mitigating bias on the ribosomal tree of life. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7785h
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