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Phylogenetic Workflows Part II: Post-tree AnalysesGiven at the Botany 2011 Conference
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Phylogenetic Workflows Part IIPost-tree Analyses
Naim MatasciThe iPlant Collaborative
Botany 2011July 8-14, 2011
Obtain sequences
•GetSeq
Obtain sequences
•GetSeq
Align sequences
•Muscle
Align sequences
•Muscle Build Tree•FastTree (aML)•Ninja (NJ)•PHYLIP (MP, NJ, ML)
Build Tree•FastTree (aML)•Ninja (NJ)•PHYLIP (MP, NJ, ML)
Visualize Tree
•iPlant Tree Viewer
Visualize Tree
•iPlant Tree Viewer
Integrate Data
•Lopper•TNRS
Integrate Data
•Lopper•TNRS
Run Analysis•CACE•DACE•Contrast•OUch•Picante•Penalized likelihood
Run Analysis•CACE•DACE•Contrast•OUch•Picante•Penalized likelihood
Merge DatasetsCombine trees, character matrices and taxa list to create new datasets
Visualize phylogeniesVisualize your data
PhylozoomExplore the Tree of Life, from the root to the leaves
Phylogenetically independent contrastsRemove the effect of shared ancestry for observed character correlations
Do traits evolve in concert?
Modified from Ackerly et al.
Contrasts
Discrete ancestral trait reconstructionInfer the state of a discrete trait along a phylogeny and estimate its rate of evolution
Ancestral state of Hawaiian lobelioids
Lobelia niihauensis: David Eickhoff, Cyanea leptostegia: Karl Magnacca
Lobelia niihauensis (Image: David Eickhoff)
Cyanea leptostegia (Image: Karl Magnacca)