221 citations · 932 across the 42 of their papers we have counts for
3 papers · 1 filter
Parametric Alignment of Drosophila Genomes
Colin Dewey, Peter Huggins, Kevin Woods +2
The classic algorithms of Needleman--Wunsch and Smith--Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). In order to process large g…
Alignment Metric Accuracy
Ariel S. Schwartz, Eugene W. Myers, Lior Pachter
We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference a…
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…