Models, algorithms and programs for phylogeny reconciliation

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses

(2011) Pawel Górecki et al.   BMC BIOINFORMATICS

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Jane: a new tool for the cophylogeny reconstruction problem

(2010) Chris Conow et al.   Algorithms for Molecular Biology

A parameter-adaptive dynamic programming approach for inferring cophylogenies

(2010) Daniel Merkle et al.   BMC BIOINFORMATICS

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

(2010) Sophie S Abby et al.   BMC BIOINFORMATICS

Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach

(2010) Ajna S Rivera et al.   BMC EVOLUTIONARY BIOLOGY

Simultaneous Identification of Duplications and Lateral Gene Transfers

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

The Cophylogeny Reconstruction Problem Is NP-Complete

(2010) Y. Ovadia et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

(2010) M. D. Rasmussen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem

(2009) Ran Libeskind-Hadas et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Space of Gene/Species Trees Reconciliations and Parsimonious Models

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

Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model

(2009) M. Csuros et al.   MOLECULAR BIOLOGY AND EVOLUTION

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

(2009) O. Akerborg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probabilistic Orthology Analysis

(2009) Bengt Sennblad et al.   SYSTEMATIC BIOLOGY

Genomes as documents of evolutionary history

(2009) Bastien Boussau et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

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

The multiple gene duplication problem revisited

(2008) M. S. Bansal et al.   BIOINFORMATICS

Birth-death prior on phylogeny and speed dating

(2008) Orjan Akerborg et al.   BMC EVOLUTIONARY BIOLOGY

Reconciliation with Non-Binary Species Trees

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