Short Read Assembly into Haplotypes. A computational
method for quantifying genetic diversity in a mixed
sample from short read sequence data and for
identifying the individual clones in the population,
while accounting for sequencing errors. See Eriksson
et al. 2008 and Zagordi et al. 2011 for details.
A machine learning package written in perl that
constructs the maximum likelihood conjunctive Bayesian
network (see Beerenwinkel, Eriksson, and Sturmfels,
2007).
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.
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).
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.