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)