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Models, algorithms and programs for phylogeny reconciliation

J.-P. Doyon, V. Ranwez, V. Daubin, V. Berry
2011 Briefings in Bioinformatics  
Existing models and algorithms of reconciliations are reviewed, and difficulties to model gene transfer are discussed.  ...  We also compare different reconciliation programs together with their advantages and disadvantages and summarize reconciliation results obtained on numerous gene families.  ...  Acknowledgments This work was supported by the French Agence Nationale de la Recherche "Domaines Emergents" [ANR-08-EMER-011, "PhylAriane"] and by the Languedoc-Roussillon's "Chercheur d'Avenir" program  ... 
doi:10.1093/bib/bbr045 pmid:21949266 fatcat:p4227fxvjrdbfflum4gxz5e5bu

Towards sub-quadratic time and space complexity solutions for the dated tree reconciliation problem

Benjamin Drinkwater, Michael A. Charleston
2016 Algorithms for Molecular Biology  
This model gives rise to a sub quadratic running time solution for the dated tree reconciliation problem for selected tree topologies, and is shown to be, in practice, the fastest method for solving the  ...  Targeted algorithmic design for specific tree topologies has to date been highly successful, with one recent formulation providing a logarithmic space complexity reduction for the dated tree reconciliation  ...  's reconciliation algorithm are both implemented in Java and run on any machine with Java 1.6 or higher.  ... 
doi:10.1186/s13015-016-0077-5 pmid:27213010 pmcid:PMC4875752 fatcat:uvzudf6s7vbu7kvwqjq3em646e

A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction [chapter]

Dannie Durand, Bjarni V. Halldórsson, Benjamin Vernot
2005 Lecture Notes in Computer Science  
The existence of a polynomial time algorithm for duplication/loss phylogeny reconstruction stands in contrast to most formulations of phylogeny reconstruction, which are NP-complete.  ...  In the first phase, a gene tree is constructed from sequence data, using any of the previously known algorithms for gene phylogeny construction.  ...  In the current work, we present a dynamic programming algorithm to find all most parsimonious phylogenies with respect to a macroevolutionary model of gene duplication and loss.  ... 
doi:10.1007/11415770_19 fatcat:jo7y44mugjfxnizpr7gtmiuelq

A Hybrid Micro–Macroevolutionary Approach to Gene Tree Reconstruction

Dannie Durand, Bjarni V. Halldórsson, Benjamin Vernot
2006 Journal of Computational Biology  
The existence of a polynomial time algorithm for duplication/loss phylogeny reconstruction stands in contrast to most formulations of phylogeny reconstruction, which are NP-complete.  ...  In the first phase, a gene tree is constructed from sequence data, using any of the previously known algorithms for gene phylogeny construction.  ...  In the current work, we present a dynamic programming algorithm to find all most parsimonious phylogenies with respect to a macroevolutionary model of gene duplication and loss.  ... 
doi:10.1089/cmb.2006.13.320 pmid:16597243 fatcat:2ujinijy6bcfnjlskfwakzglae

Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution

Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad
2004 Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04  
These MCMC algorithms take advantage of the exact algorithms for the gene evolution model. We have successfully tested our dynamical programming algorithms on real data for a biogeography problem.  ...  Third, we develop MCMC algorithms for the gene sequence evolution model that, given gene sequence data allows: (1) orthology analysis, reconciliation analysis, and gene tree reconstruction, w.r.t. a species  ...  Funding for this project was in part from the Swedish Foundation for Strategic Research, the Swedish Research Council and the Carl Trygger Foundation.  ... 
doi:10.1145/974614.974657 dblp:conf/recomb/ArvestadBLS04 fatcat:gsutgssennbc5msolzhjlwhrie

Predicting the Evolution of Syntenies—An Algorithmic Review

Nadia El-Mabrouk
2021 Algorithms  
This paper reviews some of the main algorithmic methods for inferring ancestral syntenies and focus on those integrating both gene orders and gene trees.  ...  the evolutionary model to gene insertion and deletion.  ...  Exact exponential-time algorithms based on Integer Linear Programming (ILP) [68, 69] and a polynomial-time heuristic based on dynamic programming [70] have been developed for this model, the latter  ... 
doi:10.3390/a14050152 fatcat:cqnfgv3st5a3dipcje7dcnk6wm

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem

Pawel Górecki, Oliver Eulenstein
2012 BMC Bioinformatics  
Results: We introduce the problem of reconciling unrooted and erroneous gene trees by simultaneously rooting and error-correcting them, and describe an efficient algorithm for this problem.  ...  Furthermore, the efficiency of our algorithm for error-correcting reconciliation is capable of handling truly large-scale phylogenetic studies.  ...  This work was conducted in parts with support from the Gene Tree Reconciliation Working Group at NIMBioS through NSF award #EF-0832858.  ... 
doi:10.1186/1471-2105-13-s10-s14 pmid:22759419 pmcid:PMC3382441 fatcat:7jjnfyeavrb5pkoinqwfbezsky

Unifying Parsimonious Tree Reconciliation [article]

Nicolas Wieseke, Matthias Bernt, Martin Middendorf
2013 arXiv   pre-print
Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations.  ...  We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves.  ...  We presented a O(n 2 ) time heuristic based on dynamic programming as well as an exact branch-and-bound algorithm to solve the reconciliation problem for a given X-tanglegram (S, T, φ) and cost model γ  ... 
arXiv:1307.7831v1 fatcat:e2yrtfm77rguzekvn4y6rjzcfe

iGTP: A software package for large-scale gene tree parsimony analysis

Ruchi Chaudhary, Mukul S Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein
2010 BMC Bioinformatics  
Results: We introduce iGTP, a platform-independent software program that implements state-of-the-art algorithms that greatly speed up species tree inference under the duplication, duplication-loss, and  ...  Conclusions: iGTP enables, for the first time, gene tree parsimony analyses of thousands of genes from hundreds of taxa using the duplication, duplication-loss, and deep coalescence reconciliation costs  ...  Gordon Burleigh and Minh Anh Nguyen for testing iGTP and providing extensive comments towards making the software more useful, and Michael J.  ... 
doi:10.1186/1471-2105-11-574 pmid:21092314 pmcid:PMC3002902 fatcat:uyuico3dxnhqvmmxnxvmq5njie

Evolution through segmental duplications and losses: a Super-Reconciliation approach

Mattéo Delabre, Nadia El-Mabrouk, Katharina T. Huber, Manuel Lafond, Vincent Moulton, Emmanuel Noutahi, Miguel Sautie Castellanos
2020 Algorithms for Molecular Biology  
We finally assess time efficiency of the former exponential time algorithm for the Duplication-Loss model on simulated datasets, and give a proof of concept on the opioid receptor genes.  ...  Alternatively, we show that accounting for rearrangements in the evolutionary model, but still only minimizing segmental duplication and loss events, leads to an exact polynomial-time algorithm.  ...  We also thank Sèverine Bérard and Annie Chateau for truitful discussions on the DeCo and DeCoStar algorithms that have inspired the Super-Reconciliation problem.  ... 
doi:10.1186/s13015-020-00171-4 pmid:32508979 pmcid:PMC7249433 fatcat:pjwbkxlhjbhttgncsgczlto76q

URec: a system for unrooted reconciliation

P. Gorecki, J. Tiuryn
2006 Bioinformatics  
Moreover, it computes detailed distribution of gene duplications and gene losses in a species tree. It can be used to infer optimal species phylogenies for a given set of gene trees.  ...  URec is implemented in C++ and can be easily compiled under Unix and Windows systems.  ...  Martin Vingron for constructive advise and Hannes Luz for helpful comments. Financial support is provided by KBN Grant 3 T11F 021 28.  ... 
doi:10.1093/bioinformatics/btl634 pmid:17182699 fatcat:txsx6rq2nrfyjelfvyf6z7l52u

The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome

Marina Marcet-Houben, Toni Gabaldón, Christophe d'Enfert
2009 PLoS ONE  
Finally, we discuss the implications of the high levels of topological variation for phylogeny-based orthology prediction strategies.  ...  To evaluate the representativeness of species trees based on concatenated alignments, we reconstruct several fungal species trees and compare them with the complete collection of phylogenies of genes encoded  ...  Acknowledgements We acknowledge Jaime Huerta-Cepas and other members of the department for discussions and help.  ... 
doi:10.1371/journal.pone.0004357 pmid:19190756 pmcid:PMC2629814 fatcat:iyhvewo6cve2vb2iqd3djjv5a4

The pattern and process of gene family evolution [article]

Gergely J Szöllősi, Vincent Daubin
2011 arXiv   pre-print
Finally, we use probabilistic reconciliation methods to take into consideration additional information from gene phylogenies, and find that, for prokaryotes, the majority of birth events are the result  ...  We shown that these distributions are best described by models of gene family size evolution where for individual genes the death (loss) rate is larger than the birth (duplication and transfer) rate, but  ...  This allows the construction of a dynamic programing algorithm that can efficiently sum or take the maximum over reconciliations, allowing the calculation of both equation 4 and 5.  ... 
arXiv:1102.2331v1 fatcat:mp6nbrf2yrfn7lixmzeptk2g2e

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later [chapter]

Cedric Chauve, Nadia El-Mabrouk, Laurent Guéguen, Magali Semeria, Eric Tannier
2013 Models and Algorithms for Genome Evolution  
This avenue has been poorly exploited by the community for over ten years, but recent developments allow the design of integrated methods where phylogeny informs the study of synteny and vice-versa.  ...  In a seminal book chapter published in 2000 and entitled "Duplication, Rearrangement and Reconciliation", Sankoff and El-Mabrouk outlined a general approach, making a step in that direction.  ...  Advanced models and algorithms have been developed [13, 14] (see also Chapter 6 in this volume), integrating character substitutions and indels, reconstructing phylogenies and ancestral states by various  ... 
doi:10.1007/978-1-4471-5298-9_4 fatcat:43vn2kaahvffxmmh3ckv2km53q

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

Y.-C. Wu, M. D. Rasmussen, M. S. Bansal, M. Kellis
2013 Genome Research  
Applying our algorithm to a variety of clades, including flies, fungi, and primates, as well as to simulated phylogenies, we achieve high accuracy, comparable to sophisticated probabilistic reconciliation  ...  To address these challenges, we present a novel algorithm DLCpar for inferring a most parsimonious (MP) history of a gene family in the presence of duplications, losses, and ILS.  ...  Acknowledgments We thank the MIT CompBio group for helpful comments, feedback, and discussions. This work was supported by National Science Foundation CAREER award 0644282 to M.K.  ... 
doi:10.1101/gr.161968.113 pmid:24310000 pmcid:PMC3941112 fatcat:ccke44w3zrez5fh6dtv7hqynci
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