PhylogeneticGraph (PhyG) a new phylogenetic graph search and optimization program

Parsimony optimization of phylogenetic networks

(2023) Ward C. Wheeler et al.   CLADISTICS

Distance Wagner tree refinement as a heuristic approach to character‐based initial tree construction

(2021) Ward C. Wheeler   CLADISTICS

Phylogenetic supergraphs

(2021) Ward C. Wheeler   CLADISTICS

Efficient implied alignment

(2020) Alex J. Washburn et al.   BMC BIOINFORMATICS

Comparing and displaying phylogenetic trees using edge union networks

(2019) Michael Miyagi et al.   CLADISTICS

FASTC: a file format for multi-character sequence data

(2019) Ward C. Wheeler et al.   CLADISTICS

Revising the Bantu tree

(2018) Peter M. Whiteley et al.   CLADISTICS

Phylogenetic network analysis as a parsimony optimization problem

(2015) Ward C Wheeler   BMC BIOINFORMATICS

On Computing the Maximum Parsimony Score of a Phylogenetic Network

(2015) Mareike Fischer et al.   SIAM JOURNAL ON DISCRETE MATHEMATICS

Phylogenetic Networks that Display a Tree Twice

(2014) Paul Cordue et al.   BULLETIN OF MATHEMATICAL BIOLOGY

POY version 5: phylogenetic analysis using dynamic homologies under multiple optimality criteria

(2014) Ward C. Wheeler et al.   CLADISTICS

Historical linguistics as a sequence optimization problem: the evolution and biogeography of Uto-Aztecan languages

(2014) Ward C. Wheeler et al.   CLADISTICS

Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming

(2014) Lavanya Kannan et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Local search for the generalized tree alignment problem

(2013) Andrés Varón et al.   BMC BIOINFORMATICS

Into the deep: A phylogenetic approach to the bivalve subclass Protobranchia

(2013) Prashant P. Sharma et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Counting Trees in a Phylogenetic Network Is \#P-Complete

(2013) Simone Linz et al.   SIAM JOURNAL ON COMPUTING

Maximum Parsimony on Phylogenetic networks

(2012) Lavanya Kannan et al.   Algorithms for Molecular Biology

The tree alignment problem

(2012) Andrés Varón et al.   BMC BIOINFORMATICS

Faster exact maximum parsimony search with XMP

(2011) W. Timothy J. White et al.   BIOINFORMATICS

Extended Newick: it is time for a standard representation of phylogenetic networks

(2009) Gabriel Cardona et al.   BMC BIOINFORMATICS

POY version 4: phylogenetic analysis using dynamic homologies

(2009) Andrés Varón et al.   CLADISTICS

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS