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Page 8870 of Mathematical Reviews Vol. , Issue 2000m [page]

2000 Mathematical Reviews  
, Paul Kear- ney, Ming Li [Ming Li'], Todd Wareham and Haoyong Zhang, A practical algorithm for recovering the best supported edges of an evolutionary tree (extended abstract) (287-296); Laxmi Parida,  ...  Tuza, On the complexity of bicoloring clique hypergraphs of graphs (extended abstract) (40-41); Ryan B. Hayward, Jeremy Spinrad and R.  ... 

WiSPA: A new approach for dealing with widespread parasitism [article]

Benjamin Drinkwater, Angela Qiao, Michael A. Charleston
2016 arXiv   pre-print
Recently however, well-established algorithms for estimating the problem instance where a parasite may infect only a single host have been extended to handle widespread parasites.  ...  In this work we extend these previous algorithms to handle cases where parasites inhabit phylogenetically distant hosts using an additional evolutionary event which we call spread.  ...  As there are an exponential number of possible fixed node orderings, most techniques applying this approach leverage a genetic algorithm to recover the best possible solutions in a fixed period of time  ... 
arXiv:1603.09415v1 fatcat:d5n7pft7ibdldlozik7db3lpmm

Recapitulating phylogenies using k-mers: from trees to networks

Guillaume Bernard, Mark A. Ragan, Cheong Xin Chan
2016 F1000Research  
A typical phylogenetic inference aims to capture and represent, in the form of a tree, the evolutionary history of a family of molecular sequences.  ...  Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological  ...  These scenarios cannot be captured simply in a tree or tree-like representation of evolutionary relationships.  ... 
doi:10.12688/f1000research.10225.1 pmid:28105314 pmcid:PMC5224691 fatcat:ptmte5yoebeu5cbfqh7rifrfh4

Recapitulating phylogenies using k-mers: from trees to networks

Guillaume Bernard, Mark A. Ragan, Cheong Xin Chan
2016 F1000Research  
of an organism re-trace the morphological forms of its ancestors over the course of evolution.  ...  The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes.  ...  In this network, each node represents a genome, and an edge Amendments from Version 1 In this revision, we have rewritten part of the Abstract and Introduction to clarify that (a) phylogenetic approaches  ... 
doi:10.12688/f1000research.10225.2 pmid:28105314 pmcid:PMC5224691 fatcat:powgf2hdsvhhhfjhaurusbkkke

In the Light of Deep Coalescence: Revisiting Trees Within Networks [article]

Jiafan Zhu and Yun Yu and Luay Nakhleh
2016 arXiv   pre-print
First, we extend the notion of anomaly zone to phylogenetic networks and report on anomaly results for different networks.  ...  A salient concept underlying a great majority of these developments has been the notion that a network displays a set of trees and those trees can be used to infer, analyze, and study the network.  ...  Acknowledgements This work was supported in part by grant CCF-1302179 from the National Science Foundation of the United States of America.  ... 
arXiv:1606.07350v1 fatcat:mjvylyvmjzfplpijj3yinprkbm

Systematic inference of highways of horizontal gene transfer in prokaryotes

Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten, Ron Shamir
2013 Computer applications in the biosciences : CABIOS  
Our method makes it practical, for the first time, to perform accurate highway analysis quickly and easily even on large datasets with high rates of HGT.  ...  Availability and implementation: An implementation of the method can be freely downloaded from: http://acgt.cs.tau.ac.il/hide.  ...  Step 2, for any of the In practice, the fast algorithms for PG-Norm make it possible to analyse datasets with hundreds of taxa and thousands of gene trees.  ... 
doi:10.1093/bioinformatics/btt021 pmid:23335015 fatcat:qcbu73lycjcqtkazastdlqnqti

Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies

G. Aguileta, S. Marthey, H. Chiapello, M.-H. Lebrun, F. Rodolphe, E. Fournier, A. Gendrault-Jacquemard, T. Giraud, Cécile Ané
2008 Systematic Biology  
However, for practical reasons only a few genes can be sequenced for a wide range of species.  ...  Here we asked whether we can identify a few genes, among the single-copy genes common to most fungal genomes, that are sufficient for recovering accurate and well-supported phylogenies.  ...  We thank Cécile Ané, Jack Sullivan, David Fitzpatrick, and anonymous referees for useful comments on a previous version of the manuscript.  ... 
doi:10.1080/10635150802306527 pmid:18709599 fatcat:lm7vg6nnwnfizip2hyrjvhu5ju

Inference of species phylogenies from bi-allelic markers using pseudo-likelihood

Jiafan Zhu, Luay Nakhleh
2018 Bioinformatics  
We then propose an approach for inference of phylogenetic networks based on pseudo-likelihood using bi-allelic markers.  ...  Motivation: Phylogenetic networks represent reticulate evolutionary histories. Statistical methods for their inference under the multispecies coalescent have recently been developed.  ...  Acknowledgement The authors would like to thank Heidi Meudt for sharing data for the two biological datasets.  ... 
doi:10.1093/bioinformatics/bty295 pmid:29950004 pmcid:PMC6022577 fatcat:pdvjjvmq5bfhppw6jdnwxtdila

The Emergence of Organizing Structure in Conceptual Representation

Brenden M. Lake, Neil D. Lawrence, Joshua B. Tenenbaum
2018 Cognitive Science  
While this approach can learn intuitive organizations, including a tree for animals and a ring for the color circle, it assumes a strong inductive bias that considers only these particular forms, and each  ...  Given that the inductive bias is more general, the model's initial knowledge shows little qualitative resemblance to some of the discoveries it supports.  ...  In fact, there is behavioral support for a related mechanism: people seem to be capable of identifying the abstract form of sparse relational graphs, when the edges are presented sequentially as social  ... 
doi:10.1111/cogs.12580 pmid:29315735 fatcat:dxgkkhrbvjdtlfenagunknvyzi

Correction: Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable

2019 PLoS Computational Biology  
Interestingly, however, different networks may display exactly the same set of trees, an observation that poses a problem for network reconstruction: from the perspective of many inference methods such  ...  An important way to interpret a phylogenetic network is in terms of the trees it displays, which represent all the possible histories of the characters carried by the organisms in the network.  ...  Acknowledgments We are grateful to O.Gascuel for advice on the structure of the paper. Author Contributions Wrote the paper: FP CS. Conceived the question: FP CS. Proved the main formal results: FP.  ... 
doi:10.1371/journal.pcbi.1007137 fatcat:irjuub2nizejxc6a3gy7gbsgbq

A Rooted Net of Life

David Williams, Gregory P Fournier, Pascal Lapierre, Kristen S Swithers, Anna G Green, Cheryl P Andam, J Peter Gogarten
2011 Biology Direct  
Briefly, this Rooted Net of Life genome phylogeny is constructed around an initial, well resolved and rooted tree scaffold inferred from a supermatrix of combined ribosomal genes.  ...  We present and discuss a means to incorporate much of this rich narrative into a single model that acknowledges the discrete evolutionary units that constitute the organism.  ...  tree" is best avoided.  ... 
doi:10.1186/1745-6150-6-45 pmid:21936906 pmcid:PMC3189188 fatcat:64f6e7sjnzb3dca3s7grpcwlqy

Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions

Daniel Doerr, Ilan Gronau, Shlomo Moran, Irad Yavneh
2012 Algorithms for Molecular Biology  
We provide both a theoretical derivation for this case, and a detailed simulation study on quartet trees.  ...  We introduce a theoretical framework for analyzing both sources of error based on the notion of deviation from additivity, which quantifies the contribution of model misspecification to the estimation  ...  Acknowledgements This research was supported by the Israel Science Foundation (ISF) grant No. 509/11. We also acknowledge the support for the publication fee by the  ... 
doi:10.1186/1748-7188-7-22 pmid:22938153 pmcid:PMC3538584 fatcat:vtpriaefs5avxj2bjl5477wh6a

Measuring Community Similarity with Phylogenetic Networks

Donovan H. Parks, Robert G. Beiko
2012 Molecular biology and evolution  
Here, we describe how an important class of measures including Bray-Curtis, Canberra, and UniFrac can be extended to allow community variation to be computed on a phylogenetic network.  ...  We focus on phylogenetic split systems, networks that are produced by the widely used median network and neighbor-net methods, which can represent incongruence in the evolutionary history of a set of taxa  ...  Acknowledgments This work was supported by the Killam Trusts and the Tula Foundation to D.H.P. and by Genome Atlantic, the Canada Foundation for Innovation, and the Canada Research Chairs program to R.G.B  ... 
doi:10.1093/molbev/mss200 pmid:22915830 fatcat:zn6rsbcmsndkhgrpwydsgm2jji

Stochastic Errors vs. Modeling Errors in Distance Based Phylogenetic Reconstructions [chapter]

Daniel Doerr, Ilan Gronau, Shlomo Moran, Irad Yavneh
2011 Lecture Notes in Computer Science  
We provide both a theoretical derivation for this case, and a detailed simulation study on quartet trees.  ...  We introduce a theoretical framework for analyzing both sources of error based on the notion of deviation from additivity, which quantifies the contribution of model misspecification to the estimation  ...  Acknowledgements This research was supported by the Israel Science Foundation (ISF) grant No. 509/11. We also acknowledge the support for the publication fee by the  ... 
doi:10.1007/978-3-642-23038-7_5 fatcat:ll5iuoplzndt5g5xwmb5crlnj4

Accurate prediction of orthologs in the presence of divergence after duplication [article]

Manuel Lafond, Mona Meghdari Miardan, David Sankoff
2018 bioRxiv   pre-print
Results: We formalize the notion of divergence after duplication, and provide a theoretical basis for the inference of primary and secondary orthologs.  ...  Motivation: When gene duplication occurs, one of the copies may become free of selective pressure and evolve at an accelerated pace.  ...  This was extended in later versions with the addition of the GETHOGS algorithm (Altenhoff et al., 2013; Train et al., 2017) .  ... 
doi:10.1101/294405 fatcat:6f7oezawjzbjbdl3esjvirz7f4
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