14 papers
LvD: A New Algorithm for Computing the Likelihood of a Phylogeny
David Bryant, Celine Scornavacca, David Swofford
There are few, if any, algorithms in statistical phylogenetics which are used more heavily than Felsenstein's 1973 pruning method for computing the likelihood of a tree. We present…
Parsimony and the rank of a flattening matrix
Jandre Snyman, Colin Fox, David Bryant
The standard models of sequence evolution on a tree determine probabilities for every character or site pattern. A flattening is an arrangement of these probabilities into a matrix…
The Geometry of the space of Discrete Coalescent Trees
Lena Collienne, Kieran Elmes, Mareike Fischer +2
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these date…
A 1000-fold Acceleration of Hidden Markov Model Fitting using Graphical Processing Units, with application to Nonvolcanic Tremor Classification
Marnus Stoltz, Gene Stoltz, Kazushige Obara +2
Hidden Markov models (HMMs) are general purpose models for time-series data widely used across the sciences because of their flexibility and elegance. However fitting HMMs can ofte…
Bayesian inference of species trees using diffusion models
Marnus Stoltz, Boris Bauemer, Remco Bouckaert +3
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried…
MAD roots for large trees
David Bryant, Michael Charleston
The Minimal Ancestral Deviation (MAD) method is a recently introduced procedure for estimating the root of a phylogenetic tree, based only on the shape and branch lengths of the tr…