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Page 8870 of Mathematical Reviews Vol. , Issue 2000m
[page]
2000
Mathematical Reviews
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, 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]
2016
arXiv
pre-print
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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
2016
F1000Research
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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
2016
F1000Research
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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]
2016
arXiv
pre-print
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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
2013
Computer applications in the biosciences : CABIOS
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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
2008
Systematic Biology
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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
2018
Bioinformatics
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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
2018
Cognitive Science
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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
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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
2011
Biology Direct
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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
2012
Algorithms for Molecular Biology
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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
2012
Molecular biology and evolution
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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]
2011
Lecture Notes in Computer Science
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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]
2018
bioRxiv
pre-print
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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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