Invariant Versus Classical Quartet Inference When Evolution is Heterogeneous Across Sites and Lineages

Mixture Models of Nucleotide Sequence Evolution that Account for Heterogeneity in the Substitution Process Across Sites and Across Lineages

(2014) Vivek Jayaswal et al.   SYSTEMATIC BIOLOGY

The space of phylogenetic mixtures for equivariant models

(2012) Marta Casanellas et al.   Algorithms for Molecular Biology

GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees

(2012) Anna M Kedzierska et al.   BMC BIOINFORMATICS

Generating Markov evolutionary matrices for a given branch length

(2012) Marta Casanellas et al.   LINEAR ALGEBRA AND ITS APPLICATIONS

Long Branch Effects Distort Maximum Likelihood Phylogenies in Simulations Despite Selection of the Correct Model

(2012) Patrick Kück et al.   PLoS One

Low-Parameter Phylogenetic Inference Under the General Markov Model

(2012) Barbara R. Holland et al.   SYSTEMATIC BIOLOGY

Identifiability of Large Phylogenetic Mixture Models

(2011) John A. Rhodes et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Relevant phylogenetic invariants of evolutionary models

(2010) Marta Casanellas et al.   JOURNAL DE MATHEMATIQUES PURES ET APPLIQUEES

Two Stationary Nonhomogeneous Markov Models of Nucleotide Sequence Evolution

(2010) Vivek Jayaswal et al.   SYSTEMATIC BIOLOGY

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

(2008) Julien Dutheil et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic ideals and varieties for the general Markov model

(2007) Elizabeth S. Allman et al.   ADVANCES IN APPLIED MATHEMATICS