Software

• CBN
  A machine learning package written in perl that constructs the maximum likelihood conjunctive Bayesian network (see Beerenwinkel, Eriksson, and Sturmfels, 2007).

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• treeSVD
  A collection of programs that use phylogenetic invariants to construct trees. Includes: tree building with SVD, split testing with SVD, invariants for 4 taxa, a neighbor joining implementation, and a program to simulate evolution on a tree (supports one or many rate matrices or even general transition matrices).
  Consists of 7000+ lines of C++ code using supporting libraries from Colin Dewey (www.biostat.wisc.edu/~cdewey/), SVDLIBC (tedlab.mit.edu/~dr/SVDLIBC/), and boost (www.boost.org). Version of Feb 15, 2007.
  

  • download
• riskPoly
  Computes risk polynomials - see our paper Evolution on distributive lattices for more information. Written in C.

  • download
• subAlign
  with Mathias Drton. Perl code to extract various parts of an alignment (for example, sections that are in perfect or near perfect agreement across a set of species).

  • subAlign-0.9.tar.gz
• symMarkov
  Perl code to compute the toric ideals of the Birkhoff polytopes. Computes a Markov basis for S_6 in less than two weeks - the result is a minimal generating set of 7,113,390 binomials in 720 indeterminates.

  • symMarkov-0.1.tar.gz