Data from: Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias

Liu Y, Cox CJ, Wang W, Goffinet B

Date Published: July 29, 2014

DOI: http://dx.doi.org/10.5061/dryad.7b470

 

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Title Matrix_nt_nex
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Description Matrix of nucleotide sequences of 41 mitochondrial genes for 60 streptophytes.
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Title Matrix_aa
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Description Matrix of amino acid translations of 41 mitochondrial genes for 60 streptophytes
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Title Matrix_nt_degenerate
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Description Matrix of degenerated nucleotide sequences of 41 mitochondrial genes for 60 streptophytes
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Title stmtREV_model
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Description Substitutional rate matrix of amino acid translations of mitochondrial genes of streptophytes
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Title extractdata
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Description Script used for extracting the data matrix from the SEQ-GEN output files
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Title extract_likelihood_script
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Description Script to extract likelihood scores from RAxML result
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Title Extract-CDS
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Description a Perl script for extracting mitochondrial coding genes from the GenBank file.
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Title extractdata
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Description Script used for extracting the data matrix from the SEQ-GEN output files
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Title Supplementary_Material_Liu_et_al
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Description Table S1. List of 60 taxa sampled for the mitochondrial genomic dataset in this study. Table S2. Characteristics of 41 mitochondrial genes. Table S3. Characteristics of data matrices and statistics of the best-scoring ML trees inferred from each partitioning strategy. Table S4. Average GC percentage of each plant group, and difference significance test among groups. Figure S1. The average pairwise distances of the 41mitochondrial genes. Figure S2. A summary of single gene ML tree topologies. Figure S3-S19. Supplementary trees.
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When using this data, please cite the original publication:

Liu Y, Cox CJ, Wang W, Goffinet B (2014) Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias. Systematic Biology 63(6): 862-878. http://dx.doi.org/10.1093/sysbio/syu049

Additionally, please cite the Dryad data package:

Liu Y, Cox CJ, Wang W, Goffinet B (2014) Data from: Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7b470
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