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

Damir Hasić, Eric Tannier
2019 Journal of combinatorial optimization  
We prove that the reconciliation problem including transfer and replacement is NP-hard, and that if speciations and transfers with replacement are the only allowed evolutionary events, then it is fixed-parameter  ...  We investigate models of reconciliation with a gene transfer that replaces existing gene, which is a biological important event but never included in reconciliation models.  ...  We prove that finding a minimum reconciliation that includes transfers with replacement is NP-hard.  ... 
doi:10.1007/s10878-019-00396-z fatcat:2tkm4snj6vemdgsykbbhv7scfe

Parameterized Algorithms in Bioinformatics: An Overview

Laurent Bulteau, Mathias Weller
2019 Algorithms  
This work surveys recent developments of parameterized algorithms and complexity for important NP-hard problems in bioinformatics.  ...  We cover sequence assembly and analysis, genome comparison and completion, and haplotyping and phylogenetics.  ...  Finally, we thank the anonymous reviewers for their helpful and productive comments. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/a12120256 fatcat:4dhjdnpibzh43iifgan2fu6bwa

Consistency of orthology and paralogy constraints in the presence of gene transfers [article]

Mark Jones, Manuel Lafond, Celine Scornavacca
2022 arXiv   pre-print
Namely, we show that deciding if a relation graph R is consistent with a given species network N is NP-hard, and that it is W[1]-hard under the parameter "minimum number of transfers".  ...  Such relation graphs are known to frequently contain errors, as they cannot be explained via a gene tree that both contains the depicted orthologs/paralogs, and that is consistent with a species tree S  ...  Acknowledgment Version 6 of this preprint has been peer-reviewed and recommended by Peer Community In Mathematical and Computational Biology (  ... 
arXiv:1705.01240v6 fatcat:iec4qm5zc5hclmyijvu6lkjlue

Reconciling multiple genes trees via segmental duplications and losses

Riccardo Dondi, Manuel Lafond, Celine Scornavacca
2019 Algorithms for Molecular Biology  
We show that the problem is polynomial-time solvable when δ ≤ λ (via LCA-mapping), while if δ > λ the problem is NP-hard, even when λ = 0 and a single gene tree is given, solving a long standing open problem  ...  Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently.  ...  On the other hand, we show that if δ > and both costs are given, reconciling a set of gene trees while minimizing segmental gene duplications and gene losses is NP-hard.  ... 
doi:10.1186/s13015-019-0139-6 pmid:30930955 pmcid:PMC6425616 fatcat:jluvwtr4tvc75e72o3biarspo4

Reconstructing a SuperGeneTree minimizing reconciliation

Manuel Lafond, Aïda Ouangraoua, Nadia El-Mabrouk
2015 BMC Bioinformatics  
Finally, we show that a restriction of this problem to uniquely labeled speciation gene trees, which is relevant to many biological applications, is also NP-hard.  ...  We define the supergenetree problem as finding, among all supertrees displaying a set of input gene trees, one supertree minimizing a reconciliation distance with S.  ...  Authors' contributions ML, AO, NE devised the proofs and algorithms and wrote the paper.  ... 
doi:10.1186/1471-2105-16-s14-s4 pmid:26451911 pmcid:PMC4602317 fatcat:patwvjqsfzen3ddktbb2leieza

Reconciliation and local gene tree rearrangement can be of mutual profit

Thi Nguyen, Vincent Ranwez, Stéphanie Pointet, Anne-Muriel Chifolleau, Jean-Philippe Doyon, Vincent Berry
2013 Algorithms for Molecular Biology  
Reconciliation methods compare gene trees and species trees to recover evolutionary events such as duplications, transfers and losses explaining the history and composition of genomes.  ...  Results We propose a reconciliation method accounting for gene duplications, losses and horizontal transfers, that specifically takes into account the uncertainties in gene trees by rearranging their weakly  ...  This work was funded by the french Agence Nationale de la Recherche Investissements d'avenir / Bioinformatique (ANR-10-BINF-01-02, Ancestrome), Programme 6ème Extinction (ANR-09-PEXT-000 PhyloSpace) and  ... 
doi:10.1186/1748-7188-8-12 pmid:23566548 pmcid:PMC3871789 fatcat:a75bebtylzhxbhnsyw5pxdxzxa

Gene tree species tree reconciliation with gene conversion [article]

Damir Hasic, Eric Tannier
2017 arXiv   pre-print
Gene conversion is a very frequent biological event, which results in the replacement of a gene by a copy of another from the same species and in the same gene tree.  ...  Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories.  ...  If a gene that is transfered replaces another gene, then we have transfer with replacement, which is to transfer what conversion is to duplication (see Hasić and Tannier (2017) for NP-hardness proof,  ... 
arXiv:1703.08950v2 fatcat:uzxr62mpyffyzezbytvqp7sxau

Gene tree species tree reconciliation with gene conversion

Damir Hasić, Eric Tannier
2019 Journal of Mathematical Biology  
Gene conversion is a frequent and important evolutionary event, which results in the replacement of a gene by a copy of another from the same species and in the same gene tree.  ...  Gene tree/species tree reconciliation is a recent decisive progress in phylogenetic methods, accounting for the possible differences between gene histories and species histories.  ...  If a gene that is transfered replaces another gene, then we have transfer with replacement, which is to transfer what conversion is to duplication (see Hasić and Tannier (2017) for NP-hardness proof,  ... 
doi:10.1007/s00285-019-01331-w pmid:30767052 fatcat:qy6d5sfx25eljkmzv36btp67ge

Simultaneous Identification of Duplications and Lateral Gene Transfers

A Tofigh, M Hallett, J Lagergren
2011 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
gene losses, and lateral gene transfers (also known as horizontal gene transfers).  ...  The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss.  ...  FINDING MOST PARSIMONIOUS ACYCLIC SCENARIOS IS NP-HARD In this section, we will prove that the following decision problem is NP-complete: Question: Is there an acyclic DTL-scenario for S, G, and σ with  ... 
doi:10.1109/tcbb.2010.14 pmid:21233529 fatcat:lgu2cgivkjdz3cn6ack2ox62hy

On Computing the Maximum Parsimony Score of a Phylogenetic Network

Mareike Fischer, Leo van Iersel, Steven Kelk, Celine Scornavacca
2015 SIAM Journal on Discrete Mathematics  
gene transfers.  ...  problem becomes NP-hard but is still approximable and fixed parameter tractable in the parsimony score.  ...  We can make any network tree-child and time-consistent by doing the following for each reconciliation edge (u, r): adding a node u , replacing (u, r) with two edges (u, u ) and (u , r), and adding a new  ... 
doi:10.1137/140959948 fatcat:kppgya3zhvbztosurdfsmpoo5e

Phylogenetic identification of lateral genetic transfer events

Robert G Beiko, Nicholas Hamilton
2006 BMC Evolutionary Biology  
An 'edit path' of one or more transfer events can be represented with a series of subtree prune and regraft (SPR) operations, but finding the optimal such set of operations is NP-hard for comparisons between  ...  While most of the protein trees examined here were very similar to the reference supertree, requiring zero or one edit operations for reconciliation, some trees implied up to 40 transfer events within  ...  Acknowledgements We are grateful to Mark Ragan, Timothy Harlow and Michael Höhl for helpful discussions.  ... 
doi:10.1186/1471-2148-6-15 pmid:16472400 pmcid:PMC1431587 fatcat:fh7jjs3omjfo3bhn3zt4jl3qgy

Polynomial-Time Algorithms for Phylogenetic Inference Problems [chapter]

Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami, Norbert Zeh
2018 Lecture Notes in Computer Science  
It is a variant of the well-studied Hybridization Number problem with a more generous view on which gene trees are consistent with a given species network.  ...  A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem.  ...  It NP-hard already when the input consists of only two gene trees [BS07] .  ... 
doi:10.1007/978-3-319-91938-6_4 fatcat:f4mm54g4prgdteznl5czaozsie

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

Manuel Lafond, Riccardo Dondi, Nadia El-Mabrouk
2016 Algorithms for Molecular Biology  
More specifically, we show that it is NP-Hard to edit a minimum of set of relations to make them consistent with a given species tree.  ...  We then demonstrate that editing a gene tree to satisfy a given set of relations in a minimum way is NP-Hard, where "minimum" refers either to the number of modified relations depicted by the gene tree  ...  Reconciliation [2] with the species tree then allows to infer evolutionary events (duplications and speciations) associated with the internal nodes of the gene tree.  ... 
doi:10.1186/s13015-016-0067-7 pmid:27087831 pmcid:PMC4833969 fatcat:mjqcseybljfjfccdx5ck3cgsem

Comparing reconciled gene trees in linear time

Céline Scornavacca
2020 Peer Community In Mathematical and Computational Biology  
Unlike a species tree, a gene tree results not only from speciation events, but also from events acting at the gene level, such as duplications and losses of gene copies, and gene transfer events [1] .  ...  The reconciliation of phylogenetic trees consists in embedding a given gene tree into a known species tree and, doing so, determining the location of these gene-level events on the gene tree [2] .  ...  The linear algorithm to compute the LRF distance presented in the paper has been implemented and the software -written in Python-is freely  ... 
doi:10.24072/pci.mcb.100002 fatcat:ilj34jz7ljfhjfxmzr24fbrqxe

Branch-and-Bound Approach for Parsimonious Inference of a Species Tree from a Set of Gene Family Trees [chapter]

Jean-Philippe Doyon, Cedric Chauve
2011 Advances in Experimental Medicine and Biology  
We describe a Branch-and-Bound algorithm for computing a parsimonious species tree given a set of gene family trees.  ...  Our algorithm can compute a parsimonious species tree for three cost measures: number of gene duplications, number of gene losses, and both combined.  ...  overall reconciliation cost with the whole set of input gene trees.  ... 
doi:10.1007/978-1-4419-7046-6_29 pmid:21431569 fatcat:ynwxfaiodfcxthohdfuso6hgsm
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