Difference between revisions of "Phylogenetics: Morphology and Partitioning in MrBayes"
From EEBedia
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The data for this lab comes from a paper by Nylander et al. (2004) that has already become a landmark study in combining data within a Bayesian framework. The full citation is: | The data for this lab comes from a paper by Nylander et al. (2004) that has already become a landmark study in combining data within a Bayesian framework. The full citation is: | ||
| − | Nylander, J., F. Ronquist, J. P. Huelsenbeck, and J. Nieves-Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53:47-67. | + | Nylander, J., F. Ronquist, J. P. Huelsenbeck, and J. Nieves-Aldrey. 2004. |
| + | Bayesian phylogenetic analysis of combined data. Systematic Biology 53:47-67. | ||
| − | If you have access, you can [http://taylorandfrancis.metapress.com/content/c5p30pxy4hawe7bm/fulltext.pdf download the pdf of this paper]. | + | If you have access, you can [http://taylorandfrancis.metapress.com/content/c5p30pxy4hawe7bm/fulltext.pdf download the pdf of this paper]. |
== Downloading the data file == | == Downloading the data file == | ||
The data from the paper is available in [http://www.treebase.org/treebase/index.html TreeBase] in the form of five separate files. While you can download these separately (search by Study Accession number for S970), putting them together into a single MrBayes data file is tricky (for one thing, the sequences are not in the same order in all five files!), so I have done that for you. Download the file by [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/data/nylander.nex clicking here] and save a copy to your local hard drive. | The data from the paper is available in [http://www.treebase.org/treebase/index.html TreeBase] in the form of five separate files. While you can download these separately (search by Study Accession number for S970), putting them together into a single MrBayes data file is tricky (for one thing, the sequences are not in the same order in all five files!), so I have done that for you. Download the file by [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/data/nylander.nex clicking here] and save a copy to your local hard drive. | ||
Revision as of 01:21, 9 April 2007
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EEB 349: Phylogenetics |
| The goal of this lab is twofold. First, you will learn how to analyze discrete morphological character data in MrBayes. Second, you will learn how to combine morphological with molecular data in a partitioned analysis in which each data type is assigned an appropriate model of evolution. |
The Nylander et al. study
The data for this lab comes from a paper by Nylander et al. (2004) that has already become a landmark study in combining data within a Bayesian framework. The full citation is:
Nylander, J., F. Ronquist, J. P. Huelsenbeck, and J. Nieves-Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53:47-67.
If you have access, you can download the pdf of this paper.
Downloading the data file
The data from the paper is available in TreeBase in the form of five separate files. While you can download these separately (search by Study Accession number for S970), putting them together into a single MrBayes data file is tricky (for one thing, the sequences are not in the same order in all five files!), so I have done that for you. Download the file by clicking here and save a copy to your local hard drive.
