On September 17th, the seminar participants divided into 4 groups. Each group is undertaking a project in a specific area and will present their results in the seminar. Below are descriptions of each project. If your project has progress to report, please feel free to post to the mailing list by sending email to [EMAIL PROTECTED] Please let me know if you would like something posted on the webpage.

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*** The Polyhedra & Experiments project will present on October 29th. *** This project's general theme is section 7.7, "Perturbing Tree Metrics", of _Phylogenetics_. The group is using various software packages for polyhedral computations. Serkan Hosten ([EMAIL PROTECTED]) is in charge. Josephine Yu ([EMAIL PROTECTED]) is using Polymake. Ian Sammis ([EMAIL PROTECTED]) is using Phylip. Alex Han ([EMAIL PROTECTED]) is using SplitsTree. Francisco Santos ([EMAIL PROTECTED]) and Federico Ardila ([EMAIL PROTECTED]) are also participating. Josephine Yu has created a picture of a higher-dimensional tree using Polymake. You can view it and rotate it at http://bio.math.berkeley.edu/classes/290/fa2003/PhyloPoly.html (this page is also linked from the class webpage). *** The Algebraic Invariants project will present on November 12th. *** This project's general theme is section 7.6, "Group-Valued Dissimilarities", and section 8.10, "Algebraic Dissimilarities", in _Phylogenetics_. Related papers are Hagedorn, "Determining the Number and Structure of Phylogenetic Invariants", and Evans/Speed, "Invariants of Some Probability Modes Used in Phylogenetic Inference". Kristian Ranestad ([EMAIL PROTECTED]) is in charge. Radu Mihoescu ([EMAIL PROTECTED]), Lauren Williams ([EMAIL PROTECTED]), Nick Eriksson ([EMAIL PROTECTED]), and Nicolas Bray ([EMAIL PROTECTED]) are participating. Seth Sullivant ([EMAIL PROTECTED]) and perhaps Dave Speyer ([EMAIL PROTECTED]) are semi-participating. *** The Statistics project will present on November 19th. *** This project's general theme is section 8.7, "The Felsenstein Zone", of _Phylogenetics_, and Felsenstein's book, _Inferring Phylogenies_. In their paper "Comparative Genomics via Phylogenetic Invariants for Jukes-Cantor Semigroups", Blanchette/Sankoff presented a different notion of distance between sequences, using signed permutations. The models of Thorne-Kishino-Felsenstein, Graeme Mitchison, and Ian Holmes take into account insertions & deletions in sequences. Lior Pachter ([EMAIL PROTECTED]) is in charge. David Yuchno ([EMAIL PROTECTED]) may write an undergraduate honors thesis on Thorne-Kishino-Felsenstein. Inga Hallgrimsdottir ([EMAIL PROTECTED]) and Galen Huntington ([EMAIL PROTECTED]) are participating. Samantha Reisenfeld ([EMAIL PROTECTED]) may be participating. Peter Ralph ([EMAIL PROTECTED]) may be participating. *** The Applications & Computation project will present on December 3rd. *** This project's theme is implementation of algorithms. One paper to look at is Atteson, "The Performance of Neighbor-Joining Methods of Phylogenetic Reconstruction". An interesting mathematical question arises: every algorithm for tree reconstruction defines an equivalence relation on data. So how can we describe this equivalence relation, i.e., which data will produce the same tree under this algorithm? Another paper to look at is Pachter/Speyer, "Reconstructing Trees from Subtree Weights", using m-dissimilarity maps. An interesting question is, can we *decide* whether the supposed subtree weights actually come from a tree? Another paper to look at is Billera/Holmes/Vogtmann, "Geometry of the Space of Phylogenetic Trees", on geodesics between trees. The consensus at the AIM conference in Palo Alto was that the main open problem is finding a good way to compute the distance between trees. There is a very inefficient algorithm in the paper, which should be implemented. Francis Su ([EMAIL PROTECTED]) is in charge. Nina Amenta ([EMAIL PROTECTED]), Dan Levy ([EMAIL PROTECTED]), Steve Canon ([EMAIL PROTECTED]), and Rudy Yoshida ([EMAIL PROTECTED]) are participating. Ruchira Datta ([EMAIL PROTECTED]) may be participating. Amelia Nissenbaum ([EMAIL PROTECTED]) may be participating. Susan Holmes has a package, which she will send, to compute the distance between trees. Half of the Applications & Computation Group will work on implementing the Pachter-Speyer algorithm, and the other half will work on computing convex hulls in the space of trees. Lior is providing sequence data (from fugu fish, chickens, fungi, etc.) for all of us to try out. Ruchira Datta http://math.berkeley.edu/~datta [EMAIL PROTECTED] Visit the Mathematics of Phylogenetic Trees webpage: http://bio.math.berkeley.edu/classes/290/fa2003