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Using tree diversity to compare phylogenetic heuristics

Seung-Jin Sul, Suzanne Matthews, Tiffani L Williams
2009 BMC Bioinformatics  
Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space.  ...  We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms.  ...  We also thank Matt Yoder for providing us with some of the biological datasets used in this study.  ... 
doi:10.1186/1471-2105-10-s4-s3 pmid:19426451 pmcid:PMC2681068 fatcat:ytp6f27bzzghfpl4k6p3awsnae

New Approaches to Compare Phylogenetic Search Heuristics

Seung-Jin Sul, Suzanne Matthews, Tiffani L. Williams
2008 2008 IEEE International Conference on Bioinformatics and Biomedicine  
Thus, by understanding phylogenetic heuristic behavior, better heuristics could be designed, which ultimately leads to more accurate evolutionary trees.  ...  Secondly, we develop a new entropybased measure to quantify the diversity among the evolutionary trees found by the heuristics.  ...  We also thank Matt Yoder for providing us with some of the biological datasets used in this study.  ... 
doi:10.1109/bibm.2008.81 dblp:conf/bibm/SulMW08 fatcat:glp55o3dtrh23dwfalefjdusbq

The role of diverse populations in phylogenetic analysis

Tiffani L. Williams, Marc L. Smith
2006 Proceedings of the 8th annual conference on Genetic and evolutionary computation - GECCO '06  
Currently, the bestperforming heuristic for reconstructing MP trees is Recursive-Iterative DCM3 (Rec-I-DCM3), which uses a single tree (or solution) to guide its way through an exponentially-sized tree  ...  The most popular approaches for reconstructing phylogenetic trees attempt to solve NP-hard optimization criteria such as maximum parsimony (MP).  ...  Unfortunately, the performance of these genetic algorithms are often not compared to the top performing phylogenetic heuristics.  ... 
doi:10.1145/1143997.1144046 dblp:conf/gecco/WilliamsS06 fatcat:qrckiiww6vcsnla5cqp2eyu3ku

Large-Scale Analysis of Phylogenetic Search Behavior [chapter]

Hyun Jung Park, Seung-Jin Sul, Tiffani L. Williams
2010 Advances in Experimental Medicine and Biology  
However, relatively little work has been done to analyze quantitatively the behavior of phylogenetic heuristics in tree space.  ...  Phylogenetic analysis is used in all branches of biology with applications ranging from studies on the origin of human populations to investigations of the transmission patterns of HIV.  ...  Acknowledgements The authors wish to thank Bill Murphy and Matt Yoder for providing us with the biological datasets used in this study.  ... 
doi:10.1007/978-1-4419-5913-3_5 pmid:20865484 fatcat:yu5jqegkmzfhvpwctk2we2pise

Systematic Conservation Planning for Groundwater Ecosystems Using Phylogenetic Diversity

Maria G. Asmyhr, Simon Linke, Grant Hose, David A. Nipperess, Michael Hofreiter
2014 PLoS ONE  
Here we use molecular sequence data and phylogenetic diversity as surrogates for stygofauna diversity in aquifers of New South Wales, Australia.  ...  Two molecular markers (nuclear 18S ribosomal DNA and mitochondrial cytochrome oxidase subunit I) were used to evaluate how marker variability and the resulting tree topology affected the site-selection  ...  Acknowledgments We are grateful to P. Cranidge (Gosford Council), J.P Williams, B. Mulhearn, R. Gleeson, R. Beasly, A. Pearce (New South Wales Water), P. Watson (Wyong Council), A. Michie and M.  ... 
doi:10.1371/journal.pone.0115132 pmid:25514422 pmcid:PMC4267811 fatcat:agr2am3dnbbf3by7wgb2x4rn6u

Characterizing and Comparing Phylogenies from their Laplacian Spectrum

Eric Lewitus, Helene Morlon
2015 Systematic Biology  
The ability to summarize properties of trees, compare different trees, and identify distinct modes of division within trees is essential to all these research areas.  ...  We show how to construct the spectral density profile of a phylogenetic tree from its Laplacian graph.  ...  EL would like to thank Evan Charles for helpful discussion.  ... 
doi:10.1093/sysbio/syv116 pmid:26658901 fatcat:7c5q2vqijfdvnjqh5ikdpomqhu

Characterizing and comparing phylogenies from their Laplacian spectrum [article]

Eric Lewitus, Helene Morlon
2015 bioRxiv   pre-print
The ability to summarize properties of trees, compare different trees, and identify distinct modes of division within trees is essential to all these research areas.  ...  Phylogenetic trees are central to many areas of biology, ranging from population genetics and epidemiology to microbiology, ecology, and macroevolution.  ...  We compared the principal λ, skewness, and kurtosis of spectral density profiles of each simulated tree to 4 classical measures on these trees: species richness, phylogenetic diversity, the γ statistic  ... 
doi:10.1101/026476 fatcat:w5xb55tun5bbddhfzej3z74jse

Maximising phylogenetic diversity in the selection of networks of conservation areas

Ana S.L Rodrigues, Kevin J Gaston
2002 Biological Conservation  
Phylogenetic diversity (PD) is a biodiversity measure that takes account of phylogenetic relationships (hence evolutionary history) between taxa.  ...  maximising genus diversity and PD cannot be used as evidence that the first measure is a good surrogate for the second.  ...  Williams and an anonymous referee for useful comments on the manuscript.  ... 
doi:10.1016/s0006-3207(01)00208-7 fatcat:3skxifyihnfc7ffieifpf4y3a4

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences [article]

Pierre Barbera, Alexey M. Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomas Flouri, Alexandros Stamatakis
2018 bioRxiv   pre-print
To demonstrate the scalability of EPA-ng we placed 1 billion metagenetic reads from the Tara Oceans Project onto a reference tree with 3,748 taxa in just under 7 hours, using 2,048 cores.  ...  To achieve this, phylogenetic placement methods determine how these sequences fit into an evolutionary context.  ...  More recently, we used phylogenetic nodes.  ... 
doi:10.1101/291658 fatcat:yqn52ypjjraqbacbvyxhoyr6ke

Page 130 of The Journal of Ecology Vol. 102, Issue 1 [page]

2014 The Journal of Ecology  
We also used this procedure to compare colour diversity between monocots and eudicots within the subtropical zone To visualize how evolutionary history underlies colour variation in our sample, we superimposed  ...  For the phylogenetic basis of these tests, we pruned the bird- visited species from the phylogenetic tree used in Shrestha er al. (2013b) and then merged the resulting tree with the tree of Nepali species  ... 

Computational methods for Gene Orthology inference

D. M. Kristensen, Y. I. Wolf, A. R. Mushegian, E. V. Koonin
2011 Briefings in Bioinformatics  
Identification of orthologous gene sets typically involves phylogenetic tree analysis, heuristic algorithms based on sequence conservation, synteny analysis, or some combination of these approaches.  ...  Although ideal for the purpose of orthology identification in principle, phylogenetic trees are computationally expensive to construct for large numbers of genes and genomes, and they often contain errors  ...  Ortholuge uses a phylogenetic approach to refine clusters made by a heuristic algorithm, noting cases where relative gene divergence is atypical between two compared species and an outgroup species and  ... 
doi:10.1093/bib/bbr030 pmid:21690100 pmcid:PMC3178053 fatcat:hbxflsbzc5gnrf7svljpuek7su

A heuristic approach of maximum likelihood method for inferring phylogenetic tree and an application to the mammalianSOX-3origin of the testis-determining geneSRY

Kazutaka Katoh, Takashi Miyata
1999 FEBS Letters  
This method has been applied to the inference of phylogenetic tree of the SOX family members.  ...  This model should be supported directly from the phylogenetic tree of the SOX family, but no evidence has been provided to date.  ...  Results and discussion Phylogenetic tree of the SOX family members A variety of members belonging to the SOX family have already been identi¢ed from a diverse group of vertebrates and they are classi  ... 
doi:10.1016/s0014-5793(99)01621-x pmid:10601652 fatcat:hlnugukqhnfejpzfzqe5ga73ri

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Pierre Barbera, Alexey M Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomáš Flouri, Alexandros Stamatakis
2018 Systematic Biology  
To demonstrate the scalability of EPA-NG, we placed $1$ billion metagenetic reads from the Tara Oceans Project onto a reference tree with 3748 taxa in just under $7$ h, using 2048 cores.  ...  Previous implementations of phylogenetic placement algorithms, such as the evolutionary placement algorithm (EPA) included in RAxML, or PPLACER, are being increasingly used for this purpose.  ...  suitable reference tree, and Sujatha Sunagawa for making the BV data set publicly available.  ... 
doi:10.1093/sysbio/syy054 pmid:30165689 pmcid:PMC6368480 fatcat:i6o7ky6cqjdz7i4aptttky54r4

A Fitness Distance Correlation Measure for Evolutionary Trees [chapter]

Hyun Jung Park, Tiffani L. Williams
2009 Lecture Notes in Computer Science  
These heuristics use tree score as a basis for establishing an accurate depiction of evolutionary tree relationships.  ...  As a result, most phylogenetic analyses rely on effective heuristics for obtaining accurate trees.  ...  The authors wish to thank Bill Murphy and Matt Yoder for providing us with the biological datasets used in this study.  ... 
doi:10.1007/978-3-642-00727-9_31 fatcat:3extycbdabhptfcdbenxb42mbi

Solving large scale phylogenetic problems using DCM2

D H Huson, L Vawter, T J Warnow
1999 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
We show that DCM2 can be used to accelerate searches for Maximum Parsimony trees.  ...  This is a general method which can be used with any existing phylogenetic method in order to improve its performance.  ...  Clearly, algorithms for solving large, diverse phylogenetic trees will benefit the biological community.  ... 
pmid:10786294 fatcat:hjmcz4xiivhitmk7wq33hm3piq
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