4 citations · 9 across the 5 of their papers we have counts for
5 papers
Parametric k-best alignment
Peter Huggins, Ruriko Yoshida
Optimal sequence alignments depend heavily on alignment scoring parameters. Given input sequences, {\em parametric alignment} is the well-studied problem that asks for all possible…
On the optimality of the neighbor-joining algorithm
Kord Eickmeyer, Peter Huggins, Lior Pachter +1
The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. Fro…
Partitioning the Sample Space on Five Taxa for the Neighbor Joining Algorithm
Kord Eickmeyer, Ruriko Yoshida
In this paper, we will analyze the behavior of the Neighbor Joining algorithm on five taxa and we will show that the partition of the sample (data) space for estimation of a tree t…
Neighbor joining with phylogenetic diversity estimates
Dan Levy, Ruriko Yoshida, Lior Pachter
The Neighbor-Joining algorithm is a recursive procedure for reconstructing trees that is based on a transformation of pairwise distances between leaves. We present a generalization…
Short Rational Functions for Toric Algebra and Applications
Jesus De Loera, David Haws, Raymond Hemmecke +3
We encode the binomials belonging to the toric ideal associated with an integral matrix using a short sum of rational functions as introduced by Barvinok \ci…