Data from: Supertrees based on the subtree prune-and-regraft distance

Whidden C, Zeh N, Beiko RG

Date Published: March 20, 2014

DOI: http://dx.doi.org/10.5061/dryad.h065g

 

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Title Supplemetary Figure 1
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Description Supplementary Figure 1. Inferred LGT events between 13 bacterial classes. (a) LGT heatmap. The colour side bars indicate class. The row and column order is the same. The number of transfers is shown in a white-yellow-red colour scale with darker colours indicating a higher proportion of transfer events. Colour intensity is relative to the largest number of transfers in a row. Relationships with fewer than 5% of the maximum transfer events for a row or only a single transfer event were filtered out. (b) LGT affinity graph of the bacterial classes. Each node of the graph represents a bacterial class scaled relative to the number of represented taxa (2-75). Two genera are connected by an edge if the number of inferred LGT events between them exceeds 5% of their shared genes. The shade of an edge is proportional to this ratio of LGT events to shared genes; black edges indicate relationships with at least as many LGT events as shared genes. The thickness of an edge scales relative to the actual number of inferred transfers (30-1414) with thicker edges indicating more transfers.
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Title Supplemetary Figure 2
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Description Supplementary Figure 2: The LGT affinity neighbourhood of genus Clostridium. Each node of the graph represents a bacterial genus coloured by class and scaled relative to the number of represented taxa (1-13). Two genera are connected by an edge if the number of inferred LGT events between them exceeds 5% of their shared genes. The shade of an edge is proportional to this ratio of LGT events to shared genes; black edges indicate relationships with at least as many LGT events as shared genes. The thickness of an edge scales relative to the actual number of inferred transfers (2-125) with thicker edges indicating more transfers.
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Title Supplemetary Figure 3
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Description Supplementary Figure 3: A comparison of the accuracy of SPR, RF and MRP supertrees as measured by the minimal SPR distance between simulated species histories and any rooting of the supertree under varying rates of random or divergence-biased simulated LGT events.
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Title Supplemetary Figure 4
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Description Supplementary Figure 4: One application of the cluster reduction. The subtrees on leaves 1, 2, 3, and 4 are not identical but cover the same leaf set. Thus, they can be split from the trees and solved independently. The original locations of the removed subtrees are represented by a new leaf a1 and their roots are labelled ρ1. It is preferable to cut ρ1 in any sub-MAF as we can then cut the equivalent edge above a1.
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Title EvolSimParams
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Description Example EvolSimulator configuration file used to generate simulated trees and datasets.
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Title Eukaryotic Supertrees
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Description Eukaryotic supertrees described in the main manuscript.
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Title Bacterial_trees_and_supertrees
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Description Trees and supertrees built from 244 bacterial genomes.
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When using this data, please cite the original publication:

Whidden C, Zeh N, Beiko RG (2014) Supertrees based on the subtree prune-and-regraft distance. Systematic Biology 63(4): 566-581. http://dx.doi.org/10.1093/sysbio/syu023

Additionally, please cite the Dryad data package:

Whidden C, Zeh N, Beiko RG (2014) Data from: Supertrees based on the subtree prune-and-regraft distance. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.h065g
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