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Breakpoint medians and breakpoint phylogenies: A fixed-parameter approach

J. Gramm, R. Niedermeier
2002 Bioinformatics  
In particular, we demonstrate that a simple implementation of our algorithm combined with a new tree construction heuristic allows for a new approach to breakpoint phylogeny, yielding evolutionary trees  ...  Here, we provide an exact, fixed-parameter algorithm with provable performance bounds.  ...  ACKNOWLEDGEMENTS We thank Falk Hüffner for implementing the BREAK-POINT MEDIAN algorithm, and Robert Jansen, Li-San Wang, and Tandy Warnow for making the Campanulaceae data available to us.  ... 
doi:10.1093/bioinformatics/18.suppl_2.s128 pmid:12385994 fatcat:jwv753qvqveuzhy76viaee2o7u

Multiple Genome Rearrangement and Breakpoint Phylogeny

DAVID SANKOFF, MATHIEU BLANCHETTE
1998 Journal of Computational Biology  
Based on difficulties inherent in rearrangement edit-distance calculation and interpretation, we argue for the simpler "breakpoint analysis."  ...  Tree-based multiple alignment can be achieved to a great degree of accuracy by decomposing the tree into a number of overlapping 3-stars centered on the non-terminal nodes, and solving the consensus-based  ...  ACKNOWLEDGMENTS Research supported by grants to DS from the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Canadian Genome Analysis and Technology program, and a NSERC fellowship  ... 
doi:10.1089/cmb.1998.5.555 pmid:9773350 fatcat:w3bxqps53nh75bzsafdfm5aqxm

FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data

Jason D. Bakos, Panormitis E. Elenis, Jijun Tang
2007 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering  
Our current design performs a parallelized version of the breakpoint median computation and achieves an average speedup of 876 for simulated input data having a high evolution rate.  ...  In this paper we describe our design and characterization of a co-processor architecture to accelerate median-based phylogenetic reconstruction for generearrangement data.  ...  The number of rearrangement events along each edge for each phylogeny is chosen from a uniform random distribution with range distance +/-2, where distance is a parameter.  ... 
doi:10.1109/bibe.2007.4375664 dblp:conf/bibe/BakosET07 fatcat:u2kukyy6qzhvxgumhronhrfoiu

Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data [chapter]

Bernard M. E. Moret, Adam C. Siepel, Jijun Tang, Tao Liu
2002 Lecture Notes in Computer Science  
The software used includes RevMed, developed by the authors and available at www.cs.unm.edu/∼acs/, and A. Caprara's inversion median code, generously made available for testing.  ...  The two software packages used for that purpose, BPAnalysis and GRAPPA, both use so-called breakpoint medians in their computations.  ...  Acknowledgments We thank Alberto Caprara from the Università di Bologna for letting us use his code for inversion medians.  ... 
doi:10.1007/3-540-45784-4_40 fatcat:5uniycdelvggdbyiftlaa2ilxe

New approaches for reconstructing phylogenies from gene order data

B. M.E. Moret, L.-S. Wang, T. Warnow, S. K. Wyman
2001 Bioinformatics  
We give representative results of the extensive experimentation we conducted on both real and simulated datasets in order to validate and characterize our approaches.  ...  We report on new techniques we have developed for reconstructing phylogenies on whole genomes.  ...  Bernard Moret's work was supported by NSF grant ITR 00-81404 and Tandy Warnow's work by the David and Lucile Packard Foundation.  ... 
doi:10.1093/bioinformatics/17.suppl_1.s165 pmid:11473006 fatcat:k3tkrhnmcbctnlbf2nkfua3sdq

Steps toward accurate reconstructions of phylogenies from gene-order data

Bernard M.E. Moret, Jijun Tang, Li-San Wang, Tandy Warnow
2002 Journal of computer and system sciences (Print)  
We give representative results of the extensive experimentation we conducted on both real and simulated datasets in order to validate and characterize our approaches. r  ...  We report on our progress in reconstructing phylogenies from gene-order data.  ...  Jansen for introducing us to this research area, and D. Sankoff and J. Nadeau for inviting us to the DCAF meeting, during which some of the ideas in this paper came to fruition.  ... 
doi:10.1016/s0022-0000(02)00007-7 fatcat:bxa4cuk4qvgd7bwoxgocmoracq

NoC-Based Hardware Accelerator for Breakpoint Phylogeny

Turbo Majumder, Souradip Sarkar, Partha Pratim Pande, Ananth Kalyanaraman
2012 IEEE transactions on computers  
Maximum Parsimony phylogenetic tree reconstruction is based on finding the breakpoint median, given a set of species, and is represented by a bounded edge-weight graph model.  ...  phylogeny.  ...  Special thanks to Professor Roalson for discussions and comments that helped us better our understanding of the problem from a scientific perspective.  ... 
doi:10.1109/tc.2011.100 fatcat:pvg6d4n3b5bcjgjbn6cwd4fkjy

Quartet-Based Phylogeny Reconstruction from Gene Orders [chapter]

Tao Liu, Jijun Tang, Bernard M. E. Moret
2005 Lecture Notes in Computer Science  
The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach; however, its exhaustive approach means that it can be applied only to small datasets of  ...  We give an optimization algorithm for the NP-hard problem of computing optimal trees for each quartet, present a variation of the dyadic method (using heuristics to choose suitable short quartets), and  ...  2R01GM056120-05A1 (through a subcontract to the U. of Arizona), and by the Dept. of Computer Science and Engineering at the U. of South Carolina.  ... 
doi:10.1007/11533719_9 fatcat:a2qxfzbqwjfcvf4wr6znp3mep4

A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data

M E Cosner, R K Jansen, B M Moret, L A Raubeson, L S Wang, T Warnow, S Wyman
2000 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
These same authors also developed and implemented BPAnalysis [3], a heuristic method (based upon solving many instances of the travelling salesman problem) for estimating the breakpoint phylogeny.  ...  The breakpoint phylogeny is an optimization problem proposed by Blanchette et al. for reconstructing evolutionary trees from gene order data.  ...  We were also interested in determining whether the model tree is one of the breakpoint phylogenies (and hence determine whether solving the breakpoint phylogeny is a good approach to reconstructing trees  ... 
pmid:10977071 fatcat:wnlqh4xytbbqjlqwzem5pt3a4y

MLGO: phylogeny reconstruction and ancestral inference from gene-order data

Fei Hu, Yu Lin, Jijun Tang
2014 BMC Bioinformatics  
Results: MLGO (Maximum Likelihood for Gene-Order Analysis) is a web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data.  ...  Current software and web servers typically do not support duplication and loss events along with rearrangements.  ...  FH and JT were funded by NSF IIS 1161586 and an internal grant from Tianjin University, China. YL was supported by a fellowship of the Swiss National Science Foundation (grant no.  ... 
doi:10.1186/s12859-014-0354-6 pmid:25376663 pmcid:PMC4236499 fatcat:jlp3onjzmrd2pex62uribx6loq

Reconciling molecular phylogenies with the fossil record

H. Morlon, T. L. Parsons, J. B. Plotkin
2011 Proceedings of the National Academy of Sciences of the United States of America  
When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions.  ...  To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that  ...  We then computed the median and 5% and 95% quantiles of these estimates. Fig. S2 illustrates the distribution of parameter estimates across phylogenies. Fig.  ... 
doi:10.1073/pnas.1102543108 pmid:21930899 pmcid:PMC3182748 fatcat:6wunuq34kzd5fbppjaykbehd2y

Descendants of Whole Genome Duplication within Gene Order Phylogeny

Chunfang Zheng, Qian Zhu, David Sankoff
2008 Journal of Computational Biology  
for integrating genomic distance, halving and rearrangement median algorithms.  ...  A framework for solving this difficulty requires separating out various possible local configurations of doubled and unduplicated genomes in a given phylogeny, each of which requires a different strategy  ...  GENE ORDER PHYLOGENY BASED ON ITERATIONS OF A MEDIAN ALGORITHM One of the main approaches to gene-order phylogeny is based on iterating the median algorithm to overlapping parts of a given binary branching  ... 
doi:10.1089/cmb.2008.0118 pmid:18788908 fatcat:224owa6tmjgntang32ps3p7jvi

Whole genome phylogenies reflect long-tailed distributions of recombination rates in many bacterial species [article]

Thomas Sakoparnig, Chris Field, Erik van Nimwegen
2019 bioRxiv   pre-print
Each genomic locus has been overwritten so many times by recombination that it is impossible to reconstruct the clonal phylogeny and, instead of a consensus phylogeny, the phylogeny typically changes many  ...  We find that virtually every strain has a unique pattern of recombination frequencies with other strains and that the relative rates with which different subsets of strains share SNPs follow long-tailed  ...  Acknowledgments The authors thank Olin Silander and Frederic Bertels for useful discussions during the development of this work.  ... 
doi:10.1101/601914 fatcat:vslen5s7gjcrvoq4vs5dykqoj4

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

Colin S Cooper, Rosalind Eeles, David C Wedge, Peter Van Loo, Gunes Gundem, Ludmil B Alexandrov, Barbara Kremeyer, Adam Butler, Andrew G Lynch, Niedzica Camacho, Charlie E Massie, Jonathan Kay (+60 others)
2015 Nature Genetics  
Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men.  ...  This mechanism gives rise to extensive branching evolution and cancer clone mixing as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule  ...  For the precise position of the ERG breakpoints G and H see Figure 2 . 2 Phylogenies of multi-focal prostate cancers. a-c, Phylogenies revealing the relationships between sample clones for each case.  ... 
doi:10.1038/ng.3221 pmid:25730763 pmcid:PMC4380509 fatcat:7mtd3ni3djdtljrdotol6gwg7a

Erratum: Corrigendum: Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

Colin S Cooper, Rosalind Eeles, David C Wedge, Peter Van Loo, Gunes Gundem, Ludmil B Alexandrov, Barbara Kremeyer, Adam Butler, Andrew G Lynch, Niedzica Camacho, Charlie E Massie, Jonathan Kay (+60 others)
2015 Nature Genetics  
Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men.  ...  This mechanism gives rise to extensive branching evolution and cancer clone mixing as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule  ...  ACKNOWLEDGEMENTS Patterns of ERG alterations. a-c, Circos plots highlighting ERG rearrangements present in each prostate. Each color represents a different cancer sample as indicated.  ... 
doi:10.1038/ng0615-689b pmid:26018901 fatcat:ygrw5y5c6fhsnblkoywoc4blsm
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