Data from: Origin of land plants revisited in the light of sequence contamination and missing data

 

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Title Figure-S3-54
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Description Figures S3-54: Single gene phylogenies used to validate the contamination of the charophyte sequences detected by blast search.
Download FigS3-54-Final.pdf (2.887 Mb)
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Title Figure-S55-109
Downloaded 106 times
Description Figures S55-109: Single gene phylogenies used for the congruence test.
Download FigS55-109-Final.pdf (1.790 Mb)
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Title Table-S2
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Description Table S2: Summary of the contaminations detected in the Finet et al. (2010) dataset.
Download Table_S2-Final.pdf (109.1 Kb)
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Title Table-S3
Downloaded 57 times
Description Table S3: Impact of taxon sampling on the GTR+G and CATGTR+G inferences.
Download Table_S3-Final.pdf (199.3 Kb)
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Title Complete-22360
Downloaded 11 times
Description NEXUS file: 40 taxa, 119 proteins, 22,360 unambiguously aligned amino acid positions, 11.8% of missing data.
Download Complete-22360.nex (897.3 Kb)
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Title Finet-99
Downloaded 11 times
Description NEXUS file: 77 ribosomal protein alignments of Finet et al., with 99 sequences deleted. 74 contaminant sequences were detected by the congruence test and a total of 99 sequences were removed because in 25 cases it was impossible to identify the correct sequence.
Download Finet-99.nex (938.7 Kb)
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Title Not-Complete-43300
Downloaded 12 times
Description NEXUS file: 40 taxa, 164 proteins, 43,300 unambiguously aligned amino acid positions. Ribosomal dataset (11,571 positions and 4.7 % of missing data) and non-ribosomal dataset (31,729 positions and 24.1 % of missing data).
Download Not-Complete-43300.nex (1.735 Mb)
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Title Table-S1
Downloaded 60 times
Description Table S1: Contaminations detected in alignments of Finet et al. (2010) by Blast search and by congruence test.
Download Table_S1-Final.pdf (455.7 Kb)
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Title 164-single-gene-before-SCaFoS
Downloaded 90 times
Description NEXUS files: 164 orthologous genes before the use of SCaFoS (selection of sequences, species and genes).
Download 164-single-gene-before-SCaFoS.zip (546.3 Kb)
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Title FINET-sineContam-Trees
Downloaded 86 times
Description The trees (RAxML and PhyloBayes) are inferred from the cleaned dataset (Finet-99 NEXUS file).
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Title PhyloBayes-Trees
Downloaded 91 times
Description 20 PhyloBayes trees (CATGTR+G) obtained from five different partitions (missing data) with four different taxon samples.
Download Phylobayes-Trees.zip (14.09 Kb)
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Title RAxML-Trees
Downloaded 88 times
Description 20 RAxML Best trees (GTR+G) + 20 Bipartitions (GTR+G) obtained from five different partitions (missing data) with four different taxon samples.
Download RAxML-Trees.zip (45.79 Kb)
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When using this data, please cite the original publication:

Laurin-Lemay S, Brinkmann H, Philippe H (2012) Origin of land plants revisited in the light of sequence contamination and missing data. Current Biology 22(15): R593-R594. http://dx.doi.org/10.1016/j.cub.2012.06.013

Additionally, please cite the Dryad data package:

Laurin-Lemay S, Brinkmann H, Philippe H (2012) Data from: Origin of land plants revisited in the light of sequence contamination and missing data. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hb5b0.2
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