Data from: First dating of a recombination event in mammalian tick-borne flaviviruses

 

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Title ALN1
Downloaded 70 times
Description Alignment that contains 41 complete nucleotide sequences of Tick-borne encephalitis virus and three out-groups selected among LGTV and OHFV, retrieved from Genbank in January 2011.
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Title ALN2
Downloaded 61 times
Description Alignment that contains 28 sequences from ALN1 of known collection dates (from 1937 to 2008), with the deletion of out-groups and strains with unusual sampling locations. Non coding flanking regions and gap columns were removed.
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Title ALN2_1
Downloaded 48 times
Description Alignment derived from ALN2.fas that corresponds to the putative recombinant region (204nt).
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Title ALN2_2
Downloaded 60 times
Description Alignment derived from ALN2.fas with the deletion of the putative recombinant region.
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Title ALN2_C
Downloaded 55 times
Description Alignment derived from ALN2.fas that corresponds to the C-gene region.
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Title ALN2_E
Downloaded 53 times
Description Alignment derived from ALN2.fas that corresponds to the E-gene region.
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Title ALN2_NS1
Downloaded 56 times
Description Alignment derived from ALN2.fas that corresponds to the NS1-gene region.
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Title ALN2_NS2A
Downloaded 57 times
Description Alignment derived from ALN2.fas that corresponds to the NS2A-gene region.
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Title ALN2_NS2B
Downloaded 55 times
Description Alignment derived from ALN2.fas that corresponds to the NS2B-gene region.
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Title ALN2_NS3
Downloaded 60 times
Description Alignment derived from ALN2.fas that corresponds to the NS3-gene region.
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Title ALN2_NS4A
Downloaded 57 times
Description Alignment derived from ALN2.fas that corresponds to the NS4A-gene region.
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Title ALN2_NS4B
Downloaded 59 times
Description Alignment derived from ALN2.fas that corresponds to the NS4B-gene region.
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Title ALN2_NS5
Downloaded 61 times
Description Alignment derived from ALN2.fas that corresponds to the NS5-gene region.
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Title ALN2_PrM
Downloaded 56 times
Description Alignment derived from ALN2.fas that corresponds to the PrM-gene region.
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Title ALN3
Downloaded 59 times
Description Alignment based on ALN2.fas with the deletion of the E gene and the region of NS3 identified as a possible recombinant fragment.
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Title E_161
Downloaded 56 times
Description Alignment compiled from the 161 longest E-sequences from Tick-borne encephalitis virus species available in Genbank (1033 to 1491 nt in length) endowed with sampling dates (from 1931 to 2008) retrieved in January 2011.
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Title Beast_inference1_C
Downloaded 52 times
Description Beast xml file used in Beast inference 1 for the C-gene.
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Title Beast_inference1_E
Downloaded 56 times
Description Beast xml file used in Beast inference 1 for the E-gene.
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Title Beast_inference1_NS1
Downloaded 56 times
Description Beast xml file used in Beast inference 1 for the NS1-gene.
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Title Beast_inference1_NS2A
Downloaded 51 times
Description Beast xml file used in Beast inference 1 for the NS2A-gene.
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Title Beast_inference1_NS2B
Downloaded 60 times
Description Beast xml file used in Beast inference 1 for the NS2B-gene.
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Title Beast_inference1_NS3
Downloaded 61 times
Description Beast xml file used in Beast inference 1 for the NS3-gene.
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Title Beast_inference1_NS4A
Downloaded 62 times
Description Beast xml file used in Beast inference 1 for the NS4A-gene.
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Title Beast_inference1_NS4B
Downloaded 59 times
Description Beast xml file used in Beast inference 1 for the NS4B-gene.
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Title Beast_inference1_NS5
Downloaded 61 times
Description Beast xml file used in Beast inference 1 for the NS5-gene.
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Title Beast_inference1_PrM
Downloaded 57 times
Description Beast xml file used in Beast inference 1 for the PrM-gene.
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Title Beast_inference2_ALN2_1
Downloaded 56 times
Description Beast xml file used in Beast inference 2 for the putative recombinant region of the genome.
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Title Beast_inference2_ALN2_2
Downloaded 63 times
Description Beast xml file used in Beast inference 2 for the putative non-recombinant region of the genome.
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Title Beast_inference3
Downloaded 56 times
Description Beast xml file used in Beast inference 3 based on the 28 full length ORFs with both E-gene and the recombinant fragment omitted.
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Title Beast_inference4_E_161
Downloaded 52 times
Description Beast xml file used in Beast inference 4 for analysing the 161 longest E-sequences.
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Title Figure3_a_BI
Downloaded 63 times
Description Tree file corresponding to result of the Bayesian inference reported in Figure 3a.
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Title Figure3_a_ML
Downloaded 68 times
Description Tree file corresponding to result of the Maximum Likelihood inference reported in Figure 3a.
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Title Figure3_b_BI
Downloaded 69 times
Description Tree file corresponding to result of the Bayesian inference reported in Figure 3b.
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Title Figure3_b_ML
Downloaded 62 times
Description Tree file corresponding to result of the Maximum Likelihood inference reported in Figure 3b.
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Title Beast_inference4_E_161_tree
Downloaded 66 times
Description Tree file corresponding to result of the Beast inference 4 described in Figure 5.
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When using this data, please cite the original publication:

Bertrand Y, Töpel M, Elväng A, Melik W, Johansson M (2012) First dating of a recombination event in mammalian tick-borne flaviviruses. PLoS ONE, 7(2): e31981. http://dx.doi.org/10.1371/journal.pone.0031981

Additionally, please cite the Dryad data package:

Bertrand Y, Töpel M, Elväng A, Melik W, Johansson M (2012) Data from: First dating of a recombination event in mammalian tick-borne flaviviruses. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.504636cd
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