Data from: A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates

Woodhams MD, Fernández-Sánchez J, Sumner J

Date Published: April 10, 2015

DOI: http://dx.doi.org/10.5061/dryad.461g6

 

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Title Read Me file
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Title Java_Source
Description Java source files for the likelihood analysis using Lie Markov models
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Title Lie Markov model analysis with Mathematica
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Description Various analyses of the Lie Markov models: Fourier-Motzkin elimination, nesting, equilibrium base frequencies, time reversibility, embeddability.
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Title PDF of Mathematica file
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Description Mathematica file LieMarkov.nb printed out in PDF format, to provide some accessibility to those without Mathematica.
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Title Likelihood analysis spreadsheet
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Description Spreadsheet taking output of test.sh and calculating AIC, BIC scores, ranking models, and formatting results for inclusion in the paper.
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Title Runable Java jar file for likelihood analysis
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Description See ReadMe.txt for details. Requires library jar file (https://github.com/MichaelWoodhams/pal-mdw/releases) to run.
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Title Shell script to run likelihood analysis
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Description Takes multiple days to run.
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Title Supplementary tables and figures
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Description Supplementary tables and figures in support of the main paper. Includes information repackaged from likelihoods.ods and LieMarkov.nb.
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When using this data, please cite the original publication:

Woodhams MD, Fernández-Sánchez J, Sumner JG (2015) Data from: A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates. Systematic Biology 64(4): 638-650. http://dx.doi.org/10.1093/sysbio/syv021

Additionally, please cite the Dryad data package:

Woodhams MD, Fernández-Sánchez J, Sumner J (2015) Data from: A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.461g6
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