Phylogenetic Analysis of Protein Sequence Data Using the Randomized Axelerated Maximum Likelihood (RAXML) Program
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
Phylogenetic analysis is the study of evolutionary relationships among molecules, phenotypes, and organisms. In the context of protein sequence data, phylogenetic analysis is one of the cornerstones of comparative sequence analysis and has many applications in the study of protein evolution and function. This unit provides a brief review of the principles of phylogenetic analysis and describes several different standard phylogenetic analyses of protein sequence data using the RAXML (Randomized Axelerated Maximum Likelihood) Program. Curr. Protoc. Mol. Biol. 96:19.11.1?19.11.14. © 2011 by John Wiley & Sons, Inc.
Keywords: molecular evolution; bootstrap; multiple sequence alignment; amino acid substitution matrix; evolutionary relationship; systematics
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Brief Introduction to Phylogenetic Analysis
- Phylogenetic Analysis Using the RAXML Program
- Concluding Remarks
- Literature Cited
- Figures
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PDF or HTML at Wiley Online LibraryFigures
-
Figure 19.11.1 The lazy subtree rearrangement (LSR) tree search strategy. View Image -
Figure 19.11.2 An example alignment of part of the mitochondrial cytochrome oxidase subunit II alignment in the PHYLIP format. View Image -
Figure 19.11.3 Screenshot of the (unrooted) maximum likelihood tree in the FIGTREE program. Branch lengths are in substitutions per site. View Image -
Figure 19.11.4 Examples of an unrooted (A ) and a rooted (B ) phylogenetic tree for the example data set. The unrooted tree on the top panel, if rooted on the branch leading to the Carp and Loach sequences, corresponds to the rooted tree on the bottom. Note that in the unrooted tree neighboring sequences are not necessarily closely related. View Image -
Figure 19.11.5 Different ways of visualizing bootstrap support values on phylogenetic trees. (A ) Bootstrap support values depicted on the maximum likelihood tree. (B ) The strict consensus tree, which is completely unresolved because none of the groupings was present in all bootstrap replicate trees. (C ) Bootstrap support values depicted on the majority rule tree. View Image
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