Wilke:Tutorials

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THE WILKE LAB

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Tutorials

General

• Editing pages on openwetware.org
• Using the lab cluster
• Creating publication-quality figures
• Information theory
• R tutorial videos
• Common errors in statistical analyses

Genomics and Sequence Analysis

• Notes on how to use HyPhy
• Alignment, Phylogeny, and Evolutionary Rate Analysis
• Parsing with Biopython
• Downloaded gene alignments from ensembl via Pycogent
• Tutorial on how to do independent contrasts by Dolph Schluter

Structural Biology

• Building an environment and equilibrating a PDB structure.
• Mutant screening via Steered Molecular Dynamics (SMD).
• ProDy (python) for analysis of large MD trajectories.
• Bio3d (R) for analysis of large MD trajectories.
• DSSP parser script.