Data from: Among-character rate variation distributions in phylogenetic analysis of discrete morphological characters

Harrison LB, Larsson HCE

Date Published: January 13, 2015

DOI: http://dx.doi.org/10.5061/dryad.067qg

 

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Title HarrisonLarsson_AmongCharacterRates
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Description This archive contains supporting materials for Harrison and Larsson (201X) Among-Character Rate Variation Distributions in Phylogenetic Analysis of Discrete Morphological Characters. SuppTable1.xlsx: Supplementary Table 1. List of data sets and TreeBase Accession Numbers SuppTable2.xlsx: Supplementary Table 2. Results of the main Bayesian analysis for ACRV model selection SupplementaryReferences.docx: Full references for the studies included in Supp. Table 1. MainAnalysis_MBControlFiles: MB Control files for the main analysis described in the text. NumberofRateCategoriesAnalysis_MBControlFiles: MB control files for the discrete rate category analysis. In the preceding two folders, all control files are indexed by Tree Base Accession number and by among-character rate variation model (and prior type). RScripts: folder containing R scripts (further explanation inside the .R files) 1. CombineLogExtractMCMC.R: script to process the output of MrBayes stepping-stone analysis to extract the initial MCMC portion (i.e. from the posterior) and summarize the posterior of these samples using MrBayes. 2. mb_to_beast_trees.sh: short BASH shell script to convert MrBayes formatted trees to BEAST-readable tree (used by #1, above). 3. PAUPOutputProcessor.R: R script to call PAUP* 4b10 (using Wine on Linux) and calculate per character change counts automatically given a data block (in special R format, please see the script file for details) and tree 4. PAUPLogProcessor.R: Simpler version of #3 to extract change counts from PAUP* log text file (but not call PAUP* directly). 5. S2128.rDa: the S2128 (TreeBaseID) data set in the correct R format for #3 6. S2128_Example.tree: a tree corresponding to the S2128 data set to test #3
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Title Link to modified source code for MrBayes 3.2.2-r512-SVN
Description Source Code for MrBayes 3.2.2-r512-SVN. (http://mrbayes.sourceforge.net/) modified to include the lognormal model of Among-character Rate Variation. Distributed under the GPL license, with full credit to the developers of MrBayes. Please consult the README file in the archive.
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When using this data, please cite the original publication:

Harrison LB, Larsson HCE (2015) Among-character rate variation distributions in phylogenetic analysis of discrete morphological characters. Systematic Biology 64(2): 307-324. http://dx.doi.org/10.1093/sysbio/syu098

Additionally, please cite the Dryad data package:

Harrison LB, Larsson HCE (2014) Data from: Among-character rate variation distributions in phylogenetic analysis of discrete morphological characters. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.067qg
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