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An efficient and extensible approach for compressing phylogenetic trees

Suzanne J Matthews, Tiffani L Williams
2011 BMC Bioinformatics  
TreeZip is an efficient approach for compressing large collections of phylogenetic trees.  ...  Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. TreeZip is a novel method for compressing 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

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  ...  Phylogenetic tree reconstruction is difficult in the presence of lateral gene transfer and other processes generating conflicting signals.  ...  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


R Busa-Fekete
2006 Applied Ecology and Environmental Research  
An approach of building phylogenetic trees is to define a distance function based on amino acid sequences of distinct proteins.  ...  .: Phylogenetic tree building using a novel measure -21 -APPLIED ECOLOGY AND ENVIRONMENTAL RESEARCH 4(2): 21-30. Abstract.  ...  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

The Biological Object Notation (BON): a structured file format for biological data

Jan P. Buchmann, Mathieu Fourment, Edward C. Holmes
2018 Scientific Reports  
sequences (FASTQ 2 ), phylogenetic trees (Newick 2 , NEXUS 3 ), and sequence alignments (Stockholm 4 , BAM 5 ).  ...  Here, we propose an improved format for biological data that overcomes many of the limitations associated with flat files.  ...  The biological data was compressed using the internal Python modules zlib (compression level 6) and base64. Phylogenetic data was parsed using Bio.Phylo 20 .  ... 
doi:10.1038/s41598-018-28016-6 pmid:29941895 pmcid:PMC6018389 fatcat:xxhliftwdzai3ccsdnfo6tv72a

Indexes and Computation over Compressed Structured Data (Dagstuhl Seminar 13232)

Sebastian Maneth, Gonzalo Navarro, Marc Herbstritt
2013 Dagstuhl Reports  
Extensive experiments show that the new algorithm is superior, and particularly so at the lowest memory levels and for highly repetitive data.  ...  This book provides an introduction to algorithms and data structures that operate efficiently on strings (especially those used to represent long DNA sequences).  ...  We study the problem of encoding the positions the top-k elements of an array A [1..n] for a given parameter 1 ≤ k ≤ n.  ... 
doi:10.4230/dagrep.3.6.22 dblp:journals/dagstuhl-reports/ManethN13 fatcat:b35at6erjbe63hvelnqnrt4jle

RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference [article]

Alexey Kozlov, Diego Darriba, Tomas Flouri, Benoit Morel, Alexandros Stamatakis
2018 bioRxiv   pre-print
RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability. It compares favorably to IQ-Tree, an increasingly popular recent tool for ML-based phylogenetic inference.  ...  Motivation: Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture, and medicine.  ...  We also thank Fabio Lehmann and Heinz Stockinger for the implementation and support of the RAxML-NG web server.  ... 
doi:10.1101/447110 fatcat:3pjfsixkhzanbmmvqhcb3lnob4

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Daniel L. Ayres, Aaron Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings, Andrew Rambaut, Marc A. Suchard
2011 Systematic Biology  
Most modern approaches to statistical phylogenetic inference involve computing the probability of observed character data for a set of taxa given a phylogenetic model-often a tree and continuous-time Markov  ...  inference, and GARLI (Zwickl 2006) , which uses an ML approach.  ... 
doi:10.1093/sysbio/syr100 pmid:21963610 pmcid:PMC3243739 fatcat:yjhr75hwdbdjvpeid65opwag2a

MPI-PHYLIP: Parallelizing Computationally Intensive Phylogenetic Analysis Routines for the Analysis of Large Protein Families

Alexander J. Ropelewski, Hugh B. Nicholas, Ricardo R. Gonzalez Mendez, I. King Jordan
2010 PLoS ONE  
Consensus phylogenies based on the bootstrap and other resampling methods play a crucial part in analyzing the robustness of the trees produced for these analyses.  ...  Phylogenetic study of protein sequences provides unique and valuable insights into the molecular and genetic basis of important medical and epidemiological problems as well as insights about the origins  ...  However, the manner in which bootstrapping is implemented in the PHYLIP package makes an alternative parallel approach possible without an extensive recoding.  ... 
doi:10.1371/journal.pone.0013999 pmid:21085574 pmcid:PMC2981553 fatcat:l6wiigfairgytk3caqvg34bd6u

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

John A. Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D. Bentley, Simon R. Harris
2018 Wellcome Open Research  
We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. : We recommend three approaches, depending on requirements Conclusions for accuracy and computational  ...  We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions  ...  For construction of a maximum likelihood tree, RAxML is one of the most heavily used and efficient software methods available.  ... 
doi:10.12688/wellcomeopenres.14265.2 pmid:29774245 pmcid:PMC5930550 fatcat:zhunmonr6be3nezwueh3r3a4ny

Accelerating Parallel Maximum Likelihood-Based Phylogenetic Tree Calculations Using Subtree Equality Vectors

A.P. Stamatakis, T. Ludwig, H. Meier, M.J. Wolf
2002 ACM/IEEE SC 2002 Conference (SC'02)  
We integrated our optimizations into various sequential programs and into parallel fastDNAml, one of the most common and efficient parallel programs for calculating large phylogenetic trees.  ...  Heuristics for calculating phylogenetic trees for a large sets of aligned rRNA sequences based on the maximum likelihood method are computationally expensive.  ...  Linux cluster and for his technical support.  ... 
doi:10.1109/sc.2002.10016 dblp:conf/sc/StamatakisLMW02 fatcat:yabjw3yrjfcgtata63bb4h44aq

CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes

Z. Xu, B. Hao
2009 Nucleic Acids Research  
In addition to standard phylogenetic trees, users can also choose to output trees whose monophyletic branches are collapsed to various taxonomic levels.  ...  It is more efficient and user-friendly than the previously published version in the 2004 web server issue of Nucleic Acids Research.  ...  ACKNOWLEDGEMENTS We thank Ji Qi and Hong Luo for the implementation of the 2004 version of the CVTree server.  ... 
doi:10.1093/nar/gkp278 pmid:19398429 pmcid:PMC2703908 fatcat:zw354oankrel7hujjfd4geowym

Comparison of next-generation sequencing samples using compression-based distances and its application to phylogenetic reconstruction

Ngoc Tran, Xin Chen
2014 BMC Research Notes  
Hence, in this paper we consider an alternative parameter-free approach: compression-based distance measures.  ...  In this study we perform extensive validation and show that the compression-based distances are highly consistent with those distances obtained from the k-mer based methods, from the alignment-based approach  ...  Acknowledgements This work was supported in part by the Singapore National Medical Research Council grant (CBRG11nov091) and the Singapore Ministry of Education Academic Research Fund (MOE2012-T2-1-055  ... 
doi:10.1186/1756-0500-7-320 pmid:24886411 pmcid:PMC4057587 fatcat:jebuhaqexvf4zjdissfiy5tgqm

ZARAMIT: A System for the Evolutionary Study of Human Mitochondrial DNA [chapter]

Roberto Blanco, Elvira Mayordomo
2009 Lecture Notes in Computer Science  
We have built exhaustive human mitochondrial phylogenies (∼5500 sequences) and detected problems in existing haplogroup hierarchies through datadriven classification.  ...  ZARAMIT is an information system capable of fully automated phylogeny reconstruction. Methods have been tailored to mitochondrial DNA sequences, with focus on subproblem partitioning.  ...  biological sequences, which are most often expressed as phylogenetic trees.  ... 
doi:10.1007/978-3-642-02481-8_172 fatcat:6mbfgrgaergujotgxyds75ayvy

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.  ...  An initial analysis of the results exhibits a remarkable agreement with "acceptable phylogenetic and taxonomic truth".  ...  Acknowledgements We would like to thanks Eran Bacharach, Tal Pupko, and Jacob Ziv for helpful discussions.  ... 
doi:10.1007/11415770_22 fatcat:fhdjl343eje7de2y2bheevty44

Fast algorithms for computing sequence distances by exhaustive substring composition

Alberto Apostolico, Olgert Denas
2008 Algorithms for Molecular Biology  
The increasing throughput of sequencing raises growing needs for methods of sequence analysis and comparison on a genomic scale, notably, in connection with phylogenetic tree reconstruction.  ...  The present paper describes as a paradigm the extension and efficient implementation of one of the methods in this class.  ...  Dress and B. Hao for inspiration and discussions that led to many insights.  ... 
doi:10.1186/1748-7188-3-13 pmid:18957094 pmcid:PMC2615014 fatcat:bkggpp7d4zgfjah4ajflwvewiq
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