Reconciling event-labeled gene trees with MUL-trees and species networks

Time-consistent reconciliation maps and forbidden time travel

(2018) Nikolai Nøjgaard et al.   Algorithms for Molecular Biology

Fast algorithm for the reconciliation of gene trees and LGT networks

(2017) Celine Scornavacca et al.   JOURNAL OF THEORETICAL BIOLOGY

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events

(2017) W. C. Thomas Gregg et al.   SYSTEMATIC BIOLOGY

The link between orthology relations and gene trees: a correction perspective

(2016) Manuel Lafond et al.   Algorithms for Molecular Biology

Folding and unfolding phylogenetic trees and networks

(2016) Katharina T. Huber et al.   JOURNAL OF MATHEMATICAL BIOLOGY

The mathematics of xenology: di-cographs, symbolic ultrametrics, 2-structures and tree-representable systems of binary relations

(2016) Marc Hellmuth et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Phylogenomics for Systematic Biology

(2016) David Posada   SYSTEMATIC BIOLOGY

Efficient algorithms for reconciling gene trees and species networks via duplication and loss events

(2015) Thu-Hien To et al.   BMC GENOMICS

Orthology and paralogy constraints: satisfiability and consistency

(2014) Manuel Lafond et al.   BMC GENOMICS

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

(2014) Adrian M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

Orthology Detection Combining Clustering and Synteny for Very Large Datasets

(2014) Marcus Lechner et al.   PLoS One

Do Triplets Have Enough Information to Construct the Multi-Labeled Phylogenetic Tree?

(2014) Reza Hassanzadeh et al.   PLoS One

The Inference of Gene Trees with Species Trees

(2014) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Reconciliation of Gene and Species Trees

(2014) L. Y. Rusin et al.   Biomed Research International

Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

(2013) Adrian M. Altenhoff et al.   PLoS One

Networks: expanding evolutionary thinking

(2013) Eric Bapteste et al.   TRENDS IN GENETICS

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees

(2012) Maureen Stolzer et al.   BIOINFORMATICS

Generating functions for multi-labeled trees

(2012) É. Czabarka et al.   DISCRETE APPLIED MATHEMATICS

Polynomial-Time Algorithms for Building a Consensus MUL-Tree

(2012) Yun Cui et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Orthology relations, symbolic ultrametrics, and cographs

(2012) Marc Hellmuth et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Models, algorithms and programs for phylogeny reconciliation

(2011) J.-P. Doyon et al.   BRIEFINGS IN BIOINFORMATICS

A Survey of Combinatorial Methods for Phylogenetic Networks

(2010) Daniel H. Huson et al.   Genome Biology and Evolution

Simultaneous Identification of Duplications and Lateral Gene Transfers

(2010) A Tofigh et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Inferring polyploid phylogenies from multiply-labeled gene trees

(2009) Martin Lott et al.   BMC EVOLUTIONARY BIOLOGY

Space of Gene/Species Trees Reconciliations and Parsimonious Models

(2009) Jean-Philippe Doyon et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Reconciliation with Non-Binary Species Trees

(2008) Benjamin Vernot et al.   JOURNAL OF COMPUTATIONAL BIOLOGY