Lecture GK-6

Molecular phylogeny and multiple sequence alignment

Aims

• To introduce molecular phylogeny.
• To describe methods for constructing multiple sequence alignments.

Objectives

After this lecture you will be able to:

• draw and interpret unrooted and rooted trees;
• describe and apply UPGMA, neighbour-joining and parsimony approaches to reconstructing phylogenetic trees;
• estimate branch lengths in phylogenetic trees;
• describe and apply the sum of pairs method for scoring multiple alignments;
• discuss how multi-dimensional dynamic programming can yield an optimal multiple sequence alignment;
• describe the Feng-Doolittle algorithm for progressive multiple sequence alignment.

Supplementary Material

The lecture handout, featuring some of the lecture slides, is available on-line (one per page, four per page).

• Tree of Life Explorer
• Evolution 101
• Phylogenetics Resources

References

• Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution, 4, 406-425 (local access)
• Feng, D.F. and Doolittle, R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25, 351-60 doi:10.1007/BF02603120
• Thompson, J.D., Higgins, D.G. and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research, 22, 4673-4680 doi:10.1093/nar/22.22.4673