Data from: Some limitations of public sequence data for phylogenetic inference (in plants)

Hinchliff CE, Smith SA

Date Published: July 31, 2014

DOI: http://dx.doi.org/10.5061/dryad.450qq

 

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Title Streptophytina_by_genus_alignment.phy
Downloaded 33 times
Description A phylip-format alignment file for use with the program RAxML, containing nucleotide sequence data extracted from GenBank for all available land plant genera. The partition file "Streptophytina_by_genus_partitions.part.reduced" should be used in conjunction with this one.
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Title Streptophytina_by_genus_partitions.part
Downloaded 9 times
Description A RAxML partition file to be used with the alignment file "Streptophytina_by_genus_partitions.alignment.reduced".
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Title RAxML_bestTree.generic_tree
Downloaded 24 times
Description The maximum likelihood tree topology found using the alignment file "Streptophytina_by_genus_partitions.alignment.reduced" and the partition file "Streptophytina_by_genus_partitions.part.reduced" using the parameters described in the PLoS One publication. The tree has been rooted manually.
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Title generic.ultrametric
Downloaded 30 times
Description An ultrametric chronogram generated using the program treePL and the maximum likelihood topology, as described in the PLoS One manuscript text.
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Title scripts
Downloaded 46 times
Description Python (and some other) scripts used to create figures, automate analyses, and perform other tasks related to the generation of the results as well as the manuscript itself. These are explained further internally using comments, and also discussed in the PLoS One publication.
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Title generic_tree_dated
Downloaded 14 times
Description A configuration file for treePL used to generate the "generic.ultrametric.tre" file.
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Title Supplemental tree figures
Downloaded 81 times
Description A collection of figures showing branches on generic phylogeny for which each locus contains decisive data. This Appendix is a PDF file. View its table of contents to browse the contained figures by locus name.
Download File_S1.pdf (152.9 Mb)
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When using this data, please cite the original publication:

Hinchliff CE, Smith SA (2014) Some limitations of public sequence data for phylogenetic inference (in plants). PLoS ONE 9(7): e98986. http://dx.doi.org/10.1371/journal.pone.0098986

Additionally, please cite the Dryad data package:

Hinchliff CE, Smith SA (2014) Data from: Some limitations of public sequence data for phylogenetic inference (in plants). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.450qq
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