Data from: Ancient horizontal gene transfer and the last common ancestors

Fournier GP, Andam CP, Gogarten JP

Date Published: April 23, 2015

DOI: http://dx.doi.org/10.5061/dryad.hq4gc

 

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Title Phylogenetic tree of PylRS reconstructed using PhyloBayes3.3
Downloaded 4 times
Description Phylogenetic reconstruction of PylRS sequences from the full FASTA alignment, using PhyloBayes3.3 with C60 fixed CAT site profiles.
Download File1_PylRS_PB.tree (1.938 Kb)
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Title Phylogenetic tree of SerRS/ThrRS using GUIDANCE decomposed alignment, reconstructed using PhyloBayes3.3
Downloaded 3 times
Description Phylogenetic reconstruction of SerRS/ThrRS sequences from the GUIDANCE decomposed FASTA alignment (Additional File 3) using PhyloBayes3.3 with C60 fixed CAT site profiles.
Download File2_SerThrRS_GUIDANCEDecomposed_C60_LG.con.tre (6.212 Kb)
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Title GUIDANCE decomposed alignment of SerRS/ThrRS
Downloaded 5 times
Description Decomposed alignment of sites identified by GUIDANCE as being well-aligned between and within SerRS and ThrRS paralogs (see methods).
Download File3_Aligned_SerRS_ThrRS_GUIDANCE_Decompo...fasta (97.25 Kb)
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Title Phylogenetic tree of GlyRS homodimer using GUIDANCE alignment, reconstructed using PhyloBayes3.3
Downloaded 2 times
Description Phylogenetic reconstruction of GlyRS homodimer sequences from the GUIDANCE FASTA alignment (Additional File 10) using PhyloBayes3.3 with C60 fixed CAT site profiles.
Download File4_GlyRS_Homodimer_GUIDANCE_noOut_C60_...on.tre (6.221 Kb)
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Title Phylogenetic tree of GlyRS heterodimer using GUIDANCE alignment, reconstructed using PhyloBayes3.3
Downloaded 2 times
Description Phylogenetic reconstruction of GlyRS heterodimer sequences from the GUIDANCE FASTA alignment (Additional File 11) using PhyloBayes3.3 with C60 fixed CAT site profiles.
Download File5_GlyRS_Heterodimer_GUIDANCE_noOut_PB_....tree (5.067 Kb)
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Title Aligned SerRS and ThrRS sequences
Downloaded 3 times
Description MUSCLE-aligned rare and common forms of SerRS and ThrRS protein sequences sampled across 3 Domains of life.
Download File6_Aligned_SerRS_ThrRS.fasta (272.9 Kb)
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Title Aligned GlyRS homodimer sequences
Downloaded 5 times
Description MUSCLE-aligned of GlyRS homodimer subunit protein sequences sampled across 3 Domains of life, including other aaRS outgroups
Download File7_Aligned_GlyRS_homodimer.fasta (277.1 Kb)
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Title GlyRS heterodimer subunit sequences
Downloaded 3 times
Description Concatenation of MUSCLE-aligned GlyRS heterodimer subunit protein sequences sampled across bacterial taxa, including other aaRS outgroups.
Download File8_Aligned_GlyRS_heterodimer.fasta (342.2 Kb)
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Title Aligned PylRS sequences
Downloaded 6 times
Description MUSCLE-aligned C-terminal region homologous to C-terminal subunit in bacteria, including other aaRS outgroups.
Download File9_Aligned_PylRS_Cterm.fasta (18.81 Kb)
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Title GUIDANCE selected sites of GlyRS homodimer alignment
Downloaded 2 times
Description Sites from Additional File 7 identified by GUIDANCE as being well-aligned, with single-taxon insertions removed.
Download File10_Aligned_GUIDANCE_GlyRS_homodimer.fasta (84.87 Kb)
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Title GUIDANCE selected sites of GlyRS heterodimer alignment
Downloaded 3 times
Description Sites from Additional File 8 identified by GUIDANCE as being well-aligned, with single-taxon insertions removed.
Download File11_Aligned_GUIDANCE_GlyRS_heterodimer.fasta (124.8 Kb)
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Title Maximum-likelihood (ML) tree of known PylRS homologs
Downloaded 2 times
Description Tree in Figure 1
Download Tree1_PylRS_Arc_Bac_Cterm.phy.reduced_phy...ee.txt (1.517 Kb)
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Title ML tree showing the common and rare types of SerRS and ThrRS
Downloaded 3 times
Description Tree in Figure 2
Download Tree2_Oct22014_ProfileSer1Thr2_ProfileCom...ee.txt (10.37 Kb)
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Title ML tree of the GlyRS homodimer subunit
Downloaded 2 times
Description Tree in Figure 3
Download Tree3_Oct22014_Gly_ABE_homodimer_withOutg...ee.txt (9.994 Kb)
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Title Phylogenetic analyses of the GlyRS heterodimer subunits
Downloaded 3 times
Description Tree in Figure 4
Download Tree4_Sept26_Gly_concatAlphaBeta_Bact_phe...ee.txt (8.339 Kb)
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When using this data, please cite the original publication:

Fournier GP, Andam CP, Gogarten JP (2015) Ancient horizontal gene transfer and the last common ancestors. BMC Evolutionary Biology 15: 70. http://dx.doi.org/10.1186/s12862-015-0350-0

Additionally, please cite the Dryad data package:

Fournier GP, Andam CP, Gogarten JP (2015) Data from: Ancient horizontal gene transfer and the last common ancestors. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hq4gc
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