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Best Match Graphs and Reconciliation of Gene Trees with Species Trees [article]

Manuela Geiß, Marcos E. González, Alitzel López Sánchez, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernández Rosales, Peter F. Stadler
<span title="2019-12-12">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We show that the orthology graph is a subgraph of the reciprocal best match graph (RBMG).  ...  A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches.  ...  A Extraction of Graphs from Simulated Evolutionary Scenarios The simulations of evolutionary scenarios (described in the main text) result in an event-labeled gene tree (T,t, σ ) as well as an explicit  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1904.12021v3">arXiv:1904.12021v3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kh3b2haijjajlap6etgilc7qke">fatcat:kh3b2haijjajlap6etgilc7qke</a> </span>
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Matching Bills of Materials Using Tree Reconciliation

Mohamed Kashkoush, Hoda ElMaraghy
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pg7ahjk7dvd2tinhv7p6przfy4" style="color: black;">Procedia CIRP</a> </i> &nbsp;
Recent research used graph difference operations, linear algebra and integer programming to match trees of BOM and find pairwise similarity measures for applications such as clustering product variants  ...  Matching phylogenetic trees has been utilized in biological science for decades and is retrieve the most similar design is presented.  ...  ) and a host tree (usually species tree) with the aim of properly reconstructing the evolutionary history for the associate tree to match that of the host tree.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.procir.2013.05.029">doi:10.1016/j.procir.2013.05.029</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yjiwo4v5ina4rij3g672vlcggu">fatcat:yjiwo4v5ina4rij3g672vlcggu</a> </span>
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From Best Hits to Best Matches [article]

Peter F. Stadler, Manuela Geiß, David Schaller, Alitzel López Sánchez, Marcos E. González, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernández Rosales
<span title="2020-01-03">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
(reciprocal) best match graphs and orthology relations.  ...  Improvements of tree-free orthology assessment methods can be expected from a combination of the accurate inference of best matches reported here and recent mathematical advances in the understanding of  ...  Hence, Γ is the complete graph, i.e., any gene of species σ(Y ) is correctly inferred as a best match of x.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2001.00958v1">arXiv:2001.00958v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gsv7c63d6veflbiomuu4uqbsx4">fatcat:gsv7c63d6veflbiomuu4uqbsx4</a> </span>
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Inferring Orthology and Paralogy [chapter]

Adrian M. Altenhoff, Christophe Dessimoz
<span title="">2012</span> <i title="Humana Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation.  ...  Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.  ...  Part of this chapter started as assignment for the graduate course "Reviews in Computational Biology" (263-5151-00L) at ETH Zurich.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-61779-582-4_9">doi:10.1007/978-1-61779-582-4_9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22407712">pmid:22407712</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/52mxshbwvzffrllmaipbidh5ky">fatcat:52mxshbwvzffrllmaipbidh5ky</a> </span>
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Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

Davide Heller, Damian Szklarczyk, Christian von Mering
<span title="2019-05-06">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
To resolve an inconsistency, we subsample the protein space of the OG members and perform gene tree-species tree reconciliation for each sampling.  ...  An orthologous group (OG) comprises a set of orthologous and paralogous genes that share a last common ancestor (LCA).  ...  Availability of data and materials The datasets analyzed during the current study are available in the respective eggNOG version website, i.e. for the inconsistent version (4.0) at http:// eggnog.embl.de  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-019-2828-z">doi:10.1186/s12859-019-2828-z</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ayqw4ijndrbjdpss565pf7bosu">fatcat:ayqw4ijndrbjdpss565pf7bosu</a> </span>
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Inferring Orthology and Paralogy [chapter]

Adrian M. Altenhoff, Natasha M. Glover, Christophe Dessimoz
<span title="">2019</span> <i title="Springer New York"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation.  ...  Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.  ...  Altenhoff and Natasha M. Glover contributed equally to this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-9074-0_5">doi:10.1007/978-1-4939-9074-0_5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31278664">pmid:31278664</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bfegalnlurdm3kivngq2dbhhdq">fatcat:bfegalnlurdm3kivngq2dbhhdq</a> </span>
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Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies [article]

Davide Heller, Damian Szklarczyk, Christian von Mering
<span title="2018-09-14">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
To resolve an inconsistency, we subsample the protein space of the OG members and perform gene tree-species tree reconciliation for each sampling.  ...  An orthologous group (OG) comprises a set of orthologous and paralogous genes that share a last common ancestor (LCA).  ...  Acknowledgements The authors wish to thank Jaime Huerta-Cepas, for helpful discussions and help in using the ete tookit [20] , and João F.Matias Rodrigues for helpful discussions and technical help in  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/417840">doi:10.1101/417840</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zfj2pn3ws5blxen74m4xq6pvye">fatcat:zfj2pn3ws5blxen74m4xq6pvye</a> </span>
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Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs [article]

David Schaller, Manuela Geiß, Peter F. Stadler, Marc Hellmuth
<span title="2020-11-26">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.  ...  Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match.  ...  Seemann for fruitful discussions and his helpful  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2006.02249v2">arXiv:2006.02249v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qlukurxl2bb3vlw5je7sykkr3m">fatcat:qlukurxl2bb3vlw5je7sykkr3m</a> </span>
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Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps

Nikolai Nojgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth, Marc Herbstritt
<span title="2017-08-03">2017</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/skd7nexmsvh3rjvsnwn7jyu5mm" style="color: black;">Workshop on Algorithms in Bioinformatics</a> </i> &nbsp;
We thank the organizers of the 32nd TBI Winterseminar 2017 in Bled (Slovenia), where the authors participated, met and basically drafted the main ideas of this paper, while drinking a cold and tasty red  ...  Conceptually, both the gene tree and species tree are associated with a timing of each event.  ...  From a formal point of view, a reconciliation map µ identifies vertices of a gene tree with vertices and edges in the species tree in such a way that (partial) ancestor relations given by the genes are  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4230/lipics.wabi.2017.17">doi:10.4230/lipics.wabi.2017.17</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/wabi/NojgaardGMSWH17.html">dblp:conf/wabi/NojgaardGMSWH17</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3uuyptwf7bboba4j3gjgkl5zya">fatcat:3uuyptwf7bboba4j3gjgkl5zya</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200320134823/https://findresearcher.sdu.dk:8443/ws/files/137368973/Forbidden_time_travel.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/63/d9/63d96000109111697fdcdf89993c0d5e1d8099a5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4230/lipics.wabi.2017.17"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Computational methods for Gene Orthology inference

D. M. Kristensen, Y. I. Wolf, A. R. Mushegian, E. V. Koonin
<span title="2011-06-19">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
The most direct tree-based methods typically rely on the comparison of an individual gene tree with a species tree.  ...  These approaches are faster and easier to automate than tree-based methods, with efficient implementations provided by graph-theoretical algorithms enabling comparisons of thousands of genomes.  ...  Benchmarked against COGs, reconciliation with trusted species trees, and gene order conservation [55] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbr030">doi:10.1093/bib/bbr030</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21690100">pmid:21690100</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3178053/">pmcid:PMC3178053</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hbxflsbzc5gnrf7svljpuek7su">fatcat:hbxflsbzc5gnrf7svljpuek7su</a> </span>
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Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods

Thi-Hau Nguyen, Vincent Ranwez, Vincent Berry, Celine Scornavacca, Marc Robinson-Rechavi
<span title="2013-10-04">2013</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to species trees.  ...  for a given species tree-gene tree pair.  ...  Nakhleh and the two anonymous reviewers for their helpful remarks for improving the quality of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0073667">doi:10.1371/journal.pone.0073667</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24124449">pmid:24124449</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3790797/">pmcid:PMC3790797</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mzrbnpxck5h25nfzp32lwm72lq">fatcat:mzrbnpxck5h25nfzp32lwm72lq</a> </span>
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Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs

David Schaller, Manuela Geiß, Peter F Stadler, Marc Hellmuth
<span title="2021-02-19">2021</span> <i title="Springer-Verlag"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kngnkwdthrbili3232uvzfjyyi" style="color: black;">Journal of Mathematical Biology</a> </i> &nbsp;
All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.  ...  Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match.  ...  Seemann for fruitful discussions and his helpful comments.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00285-021-01564-8">doi:10.1007/s00285-021-01564-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33606106">pmid:33606106</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7894253/">pmcid:PMC7894253</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oox4eoaqxvezjktmgsihq63aay">fatcat:oox4eoaqxvezjktmgsihq63aay</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210717151641/https://link.springer.com/content/pdf/10.1007/s00285-021-01564-8.pdf?error=cookies_not_supported&amp;code=fe8cb4d0-d2a7-4f95-9879-e3290d75125d" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cf/56/cf564e41cf7db7b1776cacedf50ae093d9cccb6f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00285-021-01564-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7894253" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The quest for orthologs: finding the corresponding gene across genomes

Arnold Kuzniar, Roeland C.H.J. van Ham, Sándor Pongor, Jack A.M. Leunissen
<span title="">2008</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/alw4ab5u3vdqlgfh3smvbfnjqu" style="color: black;">Trends in Genetics</a> </i> &nbsp;
Acknowledgements The authors are grateful to Jack Franklin and Simon Fisher for their help in shaping the manuscript and to the anonymous reviewers for their valuable comments.  ...  An orthologous group consists only of genes that have 'best' matches within the group and no 'best' matches of any gene are outside that group.  ...  matches between two species.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2008.08.009">doi:10.1016/j.tig.2008.08.009</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18819722">pmid:18819722</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4w6qrixl7naw7aoqko73vruavq">fatcat:4w6qrixl7naw7aoqko73vruavq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813044430/http://pongor.itk.ppke.hu/library/Group-Publications/PAPERS%20PDF%20ONLY/238_Kuzniar_etal2008.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c7/b7/c7b794d850bbc4cbfbe0ebd8cd74651c07aed802.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2008.08.009"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

From pairs of most similar sequences to phylogenetic best matches

Peter F. Stadler, Manuela Geiß, David Schaller, Alitzel López Sánchez, Marcos González Laffitte, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernández Rosales
<span title="2020-04-09">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/izdyn6hngbd35czi6err6qypqu" style="color: black;">Algorithms for Molecular Biology</a> </i> &nbsp;
(reciprocal) best match graphs and orthology relations.  ...  Improvements of tree-free orthology assessment methods can be expected from a combination of the accurate inference of best matches reported here and recent mathematical advances in the understanding of  ...  All authors contributed to the interpretation of results and the writing of the manuscript. All authors read and approved the final manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13015-020-00165-2">doi:10.1186/s13015-020-00165-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32308731">pmid:32308731</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7147060/">pmcid:PMC7147060</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6jy2bho3qfhxpepx23l5oj5xsy">fatcat:6jy2bho3qfhxpepx23l5oj5xsy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200410103046/https://almob.biomedcentral.com/track/pdf/10.1186/s13015-020-00165-2" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a1/7d/a17df7d69366c3365f0457a7d921a2d847a36d0c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13015-020-00165-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147060" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps [article]

Nikolai Nøjgaard, Manuela Geiß, Peter F. Stadler, Daniel Merkle, Nicolas Wieseke, Marc Hellmuth
<span title="2017-05-05">2017</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
data, i.e., without presupposed gene and species trees.  ...  Knowledge of the event labels considerably simplifies the problem of reconciling a gene tree T with a species trees S, relative to the reconciliation problem without prior knowledge of the event types.  ...  Acknowledgment We thank the organizers of the 32nd TBI Winterseminar 2017 in Bled (Slovenia), where the authors participated, met and basically drafted the main ideas of this paper, while drinking a cold  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1705.02179v1">arXiv:1705.02179v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/f7sdieo6rvbr7cyzvjtbftblei">fatcat:f7sdieo6rvbr7cyzvjtbftblei</a> </span>
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