Gene tree reconciliation including transfers with replacement is NP-hard and FPT

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Calculating the Unrooted Subtree Prune-and-Regraft Distance

(2018) Chris Whidden et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

SPR Distance Computation for Unrooted Trees

(2017) Glenn Hickey et al.   Evolutionary Bioinformatics

Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests of Multifurcating Trees

(2015) Chris Whidden et al.   ALGORITHMICA

Approximating Maximum Agreement Forest on Multiple Binary Trees

(2015) Jianer Chen et al.   ALGORITHMICA

Improved approximation algorithm for maximum agreement forest of two rooted binary phylogenetic trees

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Exploring the space of gene/species reconciliations with transfers

(2014) Yao-ban Chan et al.   JOURNAL OF MATHEMATICAL BIOLOGY

The Inference of Gene Trees with Species Trees

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

Distances between phylogenetic trees: A survey

(2014) Feng Shi et al.   TSINGHUA SCIENCE AND TECHNOLOGY

Faster exact computation of rSPR distance

(2013) Zhi-Zhong Chen et al.   JOURNAL OF COMBINATORIAL OPTIMIZATION

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss

(2013) Mukul S. Bansal et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Lateral Gene Transfer from the Dead

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

(2012) Mukul S. Bansal et al.   BIOINFORMATICS

Replacing and Additive Horizontal Gene Transfer in Streptococcus

(2012) Sang Chul Choi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lateral gene transfer as a support for the tree of life

(2012) S. S. Abby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

REPRESENTING A SET OF RECONCILIATIONS IN A COMPACT WAY

(2012) CELINE SCORNAVACCA et al.   Journal of Bioinformatics and Computational Biology

A Cluster Reduction for Computing the Subtree Distance Between Phylogenies

(2011) Simone Linz et al.   Annals of Combinatorics

Models, algorithms and programs for phylogeny reconciliation

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

Two-Stage Cooperative T Cell Receptor-Peptide Major Histocompatibility Complex-CD8 Trimolecular Interactions Amplify Antigen Discrimination

(2011) Ning Jiang et al.   IMMUNITY

A parameter-adaptive dynamic programming approach for inferring cophylogenies

(2010) Daniel Merkle et al.   BMC BIOINFORMATICS

Simultaneous Identification of Duplications and Lateral Gene Transfers

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

A practical method for exact computation of subtree prune and regraft distance

(2008) Y. Wu   BIOINFORMATICS

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS