Practical Phylogenetics

This course will use web-based and command line tools to create gene trees based on alignment of protein sequences.

This will be followed by an analysis of the trees to identify paralogous duplications and deletions. A small amount of theory will also be covered to enable participants to understand the tools used.

Course content

• Taxon sampling using Blast.
• Multiple sequence alignment using Muscle / Clustal.
• Sampling of conserved positions using Gblocks.
• Using ModelGenerator to select the best substitution model.
• Calculating trees using PhyML.
• Visualising / manipulating trees.
• Analysing trees.
• Problems of alignment formats.

Course details