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A Novel Approach for Compressing Phylogenetic Trees [chapter]

Suzanne J. Matthews, Seung-Jin Sul, Tiffani L. Williams
2010 Lecture Notes in Computer Science  
We introduce TreeZip, a novel algorithm to compress phylogenetic trees based on their shared evolutionary relationships.  ...  Our results strongly suggest that TreeZip is very effective at compressing phylogenetic trees, which allows for easier exchange of data with colleagues around the world.  ...  Acknowledgments Funding for this project was supported by NSF under grants DEB-0629849 and IIS-0713618.  ... 
doi:10.1007/978-3-642-13078-6_13 fatcat:htltzu5bazeh5mstitdpdgz3vq

PHYLOGENETIC TREE BUIL DING USING A NOVEL COMPRESSION-BASED NON-SYMMETRIC DISSIMILARITY MEASURE

R Busa-Fekete
2006 Applied Ecology and Environmental Research  
.: Phylogenetic tree building using a novel measure -21 -APPLIED ECOLOGY AND ENVIRONMENTAL RESEARCH 4(2): 21-30. Abstract.  ...  An approach of building phylogenetic trees is to define a distance function based on amino acid sequences of distinct proteins.  ...  We would also like to build a number of tree topologies at the same time in order to cover a greater part of the solution space.  ... 
doi:10.15666/aeer/0402_021030 fatcat:qnc4d4m5ibd4pcgy6p76zp53um

Alignment-free analysis of barcode sequences by means of compression-based methods

Massimo La Rosa, Antonino Fiannaca, Riccardo Rizzo, Alfonso Urso
2013 BMC Bioinformatics  
We built phylogenetic trees of every dataset, according to compression-based and classic evolutionary methods, and compared them in terms of topology preservation.  ...  In the experimental tests, we obtained scores with a percentage of similarity between evolutionary and compression-based trees between 80% and 100% for the most of datasets (94%).  ...  Declarations The publication costs for this article were funded by the CNR Interomics Flagship Project "-Development of an integrated platform for the application of "omic" sciences to biomarker definition  ... 
doi:10.1186/1471-2105-14-s7-s4 pmid:23815444 pmcid:PMC3633054 fatcat:rjf4qvml5rbvffjg6r6im4ljjy

An efficient and extensible approach for compressing phylogenetic trees

Suzanne J Matthews, Tiffani L Williams
2011 BMC Bioinformatics  
Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. TreeZip is a novel method for compressing phylogenetic trees.  ...  TreeZip is an efficient approach for compressing large collections of phylogenetic trees.  ...  Acknowledgements Funding for this project was supported by the National Science Foundation under grants DEB-0629849, IIS-0713168, and IIS-1018785.  ... 
doi:10.1186/1471-2105-12-s10-s16 pmid:22165819 pmcid:PMC3236838 fatcat:jbr42brib5btzhq25obxqromci

Prophyle: A Phylogeny-Based Metagenomic Classifier Using The Burrows-Wheeler Transform

Karel Břinda, Kamil Salikhov, Simone Pignotti, Gregory Kucherov
2017 Zenodo  
Overall, ProPhyle provides an index for resource-frugal metagenomic classification, which is accurate even with single-species phylogenetic trees.  ...  The aim of metagenomic classification is to assign each sequence of the metagenome to a corresponding taxonomic unit, or to classify it as "novel".  ...  This problem appears, in particular, with phylogenetic trees for a single species. Therefore, our objective is to store a list of associated nodes for every k-mer.  ... 
doi:10.5281/zenodo.1045426 fatcat:dxyhefzd5nfhvezebppnspfgjm

Missing the Forest for the Trees: Phylogenetic Compression and Its Implications for Inferring Complex Evolutionary Histories

Cécile Ané, Michael J. Sanderson, Mike Steel
2005 Systematic Biology  
We show not only that phylogenetic compression is an efficient method for encoding most phylogenetic data sets and is more efficient than compression schemes designed for single sequences, but also that  ...  it provides a clear information theoretic rule for determining when a collection of conflicting trees is a better explanation of the data than a single tree.  ...  Eulenstein, and Raul Piaggio for discussion of these issues, and Mike Steel, Ming Li, and an anonymous reviewer for helpful comments.  ... 
doi:10.1080/10635150590905984 pmid:15805016 fatcat:lq3znladtva7bozmjngnalcity

Information Theoretic Approaches to Whole Genome Phylogenies [chapter]

David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor
2005 Lecture Notes in Computer Science  
We describe a novel method for efficient reconstruction of phylogenetic trees, based on sequences of whole genomes or proteomes, whose lengths may greatly vary.  ...  We describe here five different applications of the method, which not only show the validity of the method, but also suggest a number of novel phylogenetic insights.  ...  Acknowledgements We would like to thanks Eran Bacharach, Tal Pupko, and Jacob Ziv for helpful discussions.  ... 
doi:10.1007/11415770_22 fatcat:fhdjl343eje7de2y2bheevty44

Whole-genome prokaryotic clustering based on gene lengths

A. Bolshoy, Z. Volkovich
2009 Discrete Applied Mathematics  
The fast-growing number of complete genome sequences prompts the development of new phylogenetic approaches.  ...  This approach is not a regular distance-based method, distinguishing it from other recently published wholegenome based clustering techniques.  ...  Acknowledgement We wish to thank Valery Kirzhner for the interest in the study and for the helpful discussions.  ... 
doi:10.1016/j.dam.2008.06.045 fatcat:7j753wf4zzdfzfe5tnffsugyda

The Average Common Substring Approach to Phylogenomic Reconstruction

Igor Ulitsky, David Burstein, Tamir Tuller, Benny Chor
2006 Journal of Computational Biology  
We describe a novel method for efficient reconstruction of phylogenetic trees, based on sequences of whole genomes or proteomes, whose lengths may greatly vary.  ...  We describe here five different applications of the method, which not only show the validity of the method, but also suggest a number of novel phylogenetic insights.  ...  ACKNOWLEDGEMENTS We would like to thanks Eran Bacharach, Tal Pupko, and Jacob Ziv for helpful discussions.  ... 
doi:10.1089/cmb.2006.13.336 pmid:16597244 fatcat:l2y4ypheo5bbncforxo55ffqdi

Phylogenetic Characterization of BKH3 Bacterium Isolated from a Hot Spring Consortium of Bakreshwar (India) and Its Application

Biswadeep Chaudhuri, Nurul Alam, Manas Sarkar, Trinath Chowdhury, Brajadulal Chattopadhyay
2016 Advances in microbiology  
Subsequent serial dilution techniques were employed to isolate pure culture of a specific bacterial strain. 16S rRNA gene sequence and phylogenetic analysis was carried out to identify the novelty of the  ...  Results: The work revealed the presence of a novel bacterial strain (BKH3; GenBank Accession No.: KP 890928) within the same hot spring consortium whose 16S rRNA gene sequence data showed 96% identity  ...  Ribo-typing and construction of phylogenetic tree.  ... 
doi:10.4236/aim.2016.66044 fatcat:moryjtfhknacfklw7mggjaclzq

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

Joel A Boyd, Ben J Woodcroft, Gene W Tyson
2018 Nucleic Acids Research  
using placement into pre-constructed gene trees.  ...  Gene-centric approaches can be used to gain a comprehensive view of diversity by examining each read independently, but traditional pairwise comparison approaches typically over-classify taxonomy and scale  ...  We thank the Australian Centre for Ecogenomics for testing and providing valuable input to GraftM.  ... 
doi:10.1093/nar/gky174 pmid:29562347 pmcid:PMC6007438 fatcat:7qutoc27jjhn3osngk5ozgw27a

Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses

D. J. Lane, B. Pace, G. J. Olsen, D. A. Stahl, M. L. Sogin, N. R. Pace
1985 Proceedings of the National Academy of Sciences of the United States of America  
Carl Woese, Robin Gutell, and Olin Kew for useful discussions and Dr. Richard Gumport for providing facilities for the synthesis of the first primer. This paper is dedicated to Carl Woese.  ...  In the first approach, phylogenetic "trees" are generated using the available 16S rRNA sequences.  ...  The relative simplicity of this approach should facilitate a rapid expansion of the 16S rRNA sequence collection available for phylogenetic analyses.  ... 
doi:10.1073/pnas.82.20.6955 pmid:2413450 pmcid:PMC391288 fatcat:q3zjcvzl75hablisggj5dpfjbq

Phylogenetic consensus networks: Computing a consensus of 1-nested phylogenetic networks [article]

Katharina T. Huber, Vincent Moulton, Andreas Spillner
2021 arXiv   pre-print
Our approach builds on a previous result by Roselló et al. that describes an encoding for any 1-nested phylogenetic network in terms of a collection of ordered pairs of subsets of (X).More specifically  ...  An important and well-studied problem in phylogenetics is to compute a consensus tree so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively  ...  Acknowledgements Huber and Moulton thank the Lorentz Center, Leiden, The Netherlands, and the organizers of the workshop "Distinguishability in Genealogical Phylogenetic Networks" held at that center in  ... 
arXiv:2107.09696v1 fatcat:4zdm67gwajbsjbybzyjtjof4yq

Can we ever identify the Urmetazoan?

B. Schierwater, R. DeSalle
2007 Integrative and Comparative Biology  
Synopsis Unraveling the root of the metazoan tree of life has been a difficult task since the time of Haeckel and the invention of phylogenetics.  ...  Here, we review the major problems of this phylogenetic conundrum and provide some directions for solving it.  ...  Acknowledgments We thank the symposium speakers in our ''Key Transitions in Animal Evolution'' symposium for discussion and the Deutsche Forschungsgemeinschaft for support (DFG-Schi 277/20-1).  ... 
doi:10.1093/icb/icm040 pmid:21669748 fatcat:mrfbe3sd6jfihnetoul4wey5ge

A novel approach to phylogenetic tree construction using stochastic optimization and clustering

Ling Qin, Yixin Chen, Yi Pan, Ling Chen
2006 BMC Bioinformatics  
Results: A new phylogenetic tree construction method from a given set of objects (proteins, species, etc.) is presented.  ...  As an extension of ant colony optimization, this method proposes an adaptive phylogenetic clustering algorithm based on a digraph to find a tree structure that defines the ancestral relationships among  ...  Acknowledgements This paper is supported in part by a US Department of Energy ECPI grant, the Chinese National Natural Science Foundation under grant No.  ... 
doi:10.1186/1471-2105-7-s4-s24 pmid:17217517 pmcid:PMC1780127 fatcat:7yrumjpzafcxrprky3cmymypf4
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