Course Schedule

High Throughput Multiple Alignment: MUSCLE

A Fast Heuristic: BLAST

Reliable Workhorse: CLUSTALX

Bayesian Phylogenetics: MrBayes

Ribosomal RNA Alignment: ARB

Phylogenetic Networks: SplitsTree4

Accurate Multiple Alignment: ProbCons

Relaxed Bayesian Phylogenetics: BEAST

Workshops and Conferences

Phylogenetic Networks: SplitsTree4

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Related Files

» Lecture 7: Consensus Networks and Super-Networks (Compressed File, 1MB)

» SplitsTree4 Manual

» Phylogenetic Super-Networks from Partial Trees (Huson et al)

» Reconstruction of Reticulate Networks from Gene Trees (Huson et al)

Lectures (8-10-06 and 8-15-06)

Lecture 7. Consensus Networks and Super-Networks. (August 10, 2006). (Download from "Related Files.")

Lecture 8. The SplitsTree4 package, Reticulate Networks, and Hybridization Networks. (August 15, 2006). To appear.

Software Package: SplitsTree4

SplitsTree4 Homepage.
SplitsTree4 Manual (Download from "Related Files")

Foundation paper and tutorial:

Huson, D. and D. Bryant. 2006. Applications of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, 23(2): 254-267.
Huson, D. 2005. ISMB Tutorial: Introduction to Phylogenetic Networks.

Related Papers (Links):

Holland, B.R. et al. 2004. Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny. Molecular Biology and Evolution, 21(7) : 259-261.
Holland, B.R. et al. 2005. Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods. Systematic Biology, 54(1) : 66-76.
Holland, B. and V. Moulton. 2006. Consensus networks: A method for visualising incompatibilities in collections of trees. (Preprint)

Related Papers (Download from "Related Files"):

Huson, D. et al. 2004. "Phylogenetic Super-Networks from Partial Trees" IEEE Transactions on Computational Biology and Bioinformatics, 1(4) : 151-158.
Huson, D.H. et al. 2005. "Reconstruction of Reticulate Networks from Gene Trees," In S. Miyano et al (eds.) RECOMB 2005, Lecture Notes in Bioinformatics, pp. 233-249. Springer-Verlag, Berlin and Heidelberg.

Last updated August 13, 2006
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