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A GLOBAL MAXIMUM LIKELIHOOD SUPER-QUARTET PHYLOGENY METHOD

P. WANG, B. B. ZHOU, M. TARAENEH, D. CHU, C. WANG, A. Y. ZOMAYA, R. P. BRENT
2007 Proceedings of the 5th Asia-Pacific Bioinformatics Conference  
Extending the idea of our previous algorithm [17, 18] we developed a new sequential quartet-based phylogenetic tree construction method.  ...  This new algorithm reconstructs the phylogenetic tree iteratively by examining at each merge step every possible super-quartet which is formed by four subtrees instead of simple quartet in our previous  ...  Therefore reconstruction of phylogenetic trees from molecular sequences has strong research significance. The quartet-based approach is one of the primary methods for phylogeny reconstruction.  ... 
doi:10.1142/9781860947995_0014 fatcat:cqql6fo55jdlpguitz3nvpf67e

Fast error-tolerant quartet phylogeny algorithms [article]

Daniel G. Brown, Jakub Truszkowski
2010 arXiv   pre-print
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet  ...  Our incremental algorithm relies upon a search tree structure for the phylogeny that is balanced, with high probability, no matter what the true topology is.  ...  The algorithm runs in O(n log n) time, which is the lower bound for any phylogeny reconstruction algorithm. Our prototype implementation seems reasonably fast on both real and simulated datasets.  ... 
arXiv:1010.1866v1 fatcat:7mfktjlcfzg65ddt3xfc4wicma

Towards a practical O(nlogn) phylogeny algorithm

Jakub Truszkowski, Yanqi Hao, Daniel G Brown
2012 Algorithms for Molecular Biology  
Our results suggest a new direction for quartet-based phylogenetic reconstruction that may yield striking speed improvements at minimal accuracy cost.  ...  Our algorithm has high probability of returning the correct phylogeny when quartet errors are independent and occur with known probability, and when the algorithm uses a guide tree on O(log log n) taxa  ...  award to YH; from the Province of Ontario through an Early Researcher Award to DGB; and from a Cheriton Scholarship to JT.  ... 
doi:10.1186/1748-7188-7-32 pmid:23181935 pmcid:PMC3561654 fatcat:4gqpmnmcjrhsxdwuxtlw7ammqa

Towards a Practical O(n logn) Phylogeny Algorithm [chapter]

Daniel G. Brown, Jakub Truszkowski
2011 Lecture Notes in Computer Science  
Our results suggest a new direction for quartet-based phylogenetic reconstruction that may yield striking speed improvements at minimal accuracy cost.  ...  Our algorithm has high probability of returning the correct phylogeny when quartet errors are independent and occur with known probability, and when the algorithm uses a guide tree on O(log log n) taxa  ...  award to YH; from the Province of Ontario through an Early Researcher Award to DGB; and from a Cheriton Scholarship to JT.  ... 
doi:10.1007/978-3-642-23038-7_2 fatcat:sk4axi4n7zai5dlthqrzhzqq3m

A Stochastic Local Search algorithm for distance-based phylogeny reconstruction [article]

F. Tria, E. Caglioti, V. Loreto, A. Pagnani
2010 arXiv   pre-print
In distance-based reconstruction methods, two properties of additive distances were extensively exploited as antagonist criteria to drive phylogeny reconstruction: on the one hand a local property of quartets  ...  When tested on artificially generated phylogenies our Stochastic Big-Quartet Swapping algorithmic scheme significantly outperforms state-of-art distance-based algorithms in cases of deviation from additivity  ...  DISCUSSION AND CONCLUSIONS In this paper we have introduced a new algorithmic scheme for phylogeny reconstruction.  ... 
arXiv:1002.1100v1 fatcat:r5aafxwwlre65fctkebytxevsm

Fast reconstruction of phylogenetic trees using locality-sensitive hashing [article]

Daniel G. Brown, Jakub Truszkowski
2012 arXiv   pre-print
Our new algorithm runs in $O(n^{1+\gamma(g)}\log^2n)$ time, where $\gamma$ is an increasing function of an upper bound on the branch lengths in the phylogeny, the upper bound $g$ must be below$1/2-\sqrt  ...  Via a prototype and a sequence of large-scale experiments, we show that many large phylogenies can be reconstructed fast, without compromising reconstruction accuracy.  ...  Conclusions and future work We have presented a fast theoretical algorithm that correctly reconstructs phylogenies whose branch lengths are short enough.  ... 
arXiv:1111.0379v2 fatcat:3jufuol2ynghjeqxeli2l37r24

Reconstructing Optimal Phylogenetic Trees: A Challenge in Experimental Algorithmics [chapter]

Bernard M. E. Moret, Tandy Warnow
2002 Lecture Notes in Computer Science  
The second use focused on experimentation: we conducted an extensive study of quartet-based reconstruction algorithms within a parameter-rich simulation space, using several hundred CPU-years of computation  ...  In this paper, we present on one such application: the reconstruction of evolutionary histories (phylogenies) from molecular data such as DNA sequences.  ...  In developing such an understanding, the reconstruction of phylogenies is a crucial tool, as it allows one to test new models of evolution.  ... 
doi:10.1007/3-540-36383-1_8 fatcat:e5cnd5uqi5fdpdjczq7o2tf5re

Quartet-Based Phylogeny Reconstruction with Answer Set Programming

Gang Wu, Jia-huai You, Guohui Lin
2007 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
The experimental results on a number of simulated datasets suggest that the new representation combined with answer set programming presents a unique perspective to the MQC problem.  ...  In this paper, a new representation is presented for the Maximum Quartet Consistency (MQC) problem, where solving the MQC problem becomes searching for an ultrametric matrix that satisfies a maximum number  ...  Quartet-Based Phylogeny Reconstruction In the last two decades, quartet-based methods for reconstructing phylogenies have received a considerable amount of attention in the computational biology community  ... 
doi:10.1109/tcbb.2007.1008 pmid:17277421 fatcat:3z7wrpy5aresbgrlvftwechzdq

Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis [chapter]

Sebastien Roch, Sagi Snir
2012 Lecture Notes in Computer Science  
Our results, which are optimal up to logarithmic factors, are based on the analysis of a robust, computationally efficient reconstruction method and provides insight into the design of such methods.  ...  Under a model of randomly distributed LGT, we show that the species phylogeny can be reconstructed even in the presence of surprisingly many (almost linear number of) LGT events per gene tree.  ...  This result is based on a polynomial-time algorithm we describe in Section 3. Remark 8 (Number of genes).  ... 
doi:10.1007/978-3-642-29627-7_23 fatcat:n3bjp5lol5b3tgwzmiffm26qea

FASTER SOLUTION TO THE MAXIMUM QUARTET CONSISTENCY PROBLEM WITH CONSTRAINT PROGRAMMING

GANG WU, GUOHUI LIN, JIA-HUAI YOU, XIAOMENG WU
2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
A quartet approach is to build a local phylogeny for every 4 species, which is called a quartet for these 4 species, and then to assemble a phylogeny for the whole set of species satisfying the topological  ...  The experimental results on both the simulated and real datasets suggest that the new representation combined with Constraint Programming presents a unique perspective to the MQC problem.  ...  reconstruction is to first build a subtree of phylogeny for every subset of 4 species (quartet) and then rely on some combinatorial algorithms to construct a phylogeny on the entire set of species.  ... 
doi:10.1142/9781860947322_0033 fatcat:ov3uikv36zbgtlkwgq3oa6667y

Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis

Sebastien Roch, Sagi Snir
2013 Journal of Computational Biology  
Preliminary results were announced without proof in the proceedings of RECOMB 2012. to logarithmic factors, are based on the analysis of a robust, computationally efficient reconstruction method and provides  ...  Our results, which are optimal up * Keywords: Phylogenetic Reconstruction, Lateral Gene Transfer, Quartet Reconstruction.  ...  Because we first recover the species phylogeny, our highway reconstruction algorithm does not require a trusted species tree.  ... 
doi:10.1089/cmb.2012.0234 pmid:23383996 pmcid:PMC3576915 fatcat:yzlipxdfsnfkhlexiolymxprhu

Quartet-Based Phylogenetic Inference: Improvements and Limits

Vincent Ranwez, Olivier Gascuel
2001 Molecular biology and evolution  
We present weight optimization (WO), a new algorithm which is also based on weighted 4-trees. WO is faster and offers better theoretical guarantees than QP.  ...  These methods first compute fourtaxon trees (4-trees) and then use a combinatorial algorithm to infer a phylogeny that respects the inferred 4-trees as much as possible.  ...  Conclusions We have presented a new phylogenetic reconstruction algorithm based on weighted 4-trees.  ... 
doi:10.1093/oxfordjournals.molbev.a003881 pmid:11371598 fatcat:v6ofs2w5ubb2naew4wjrumvobu

Multi-SpaM: a Maximum-Likelihood approach to Phylogeny reconstruction based on Multiple Spaced-Word Matches [article]

Thomas Dencker, Chris-Andre Leimeister, Michael Gerth, Christoph Bleidorn, Sagi Snir, Burkhard Morgenstern
2018 arXiv   pre-print
Results: In this paper, we propose the first word-based approach to tree reconstruction that is based on multiple sequence comparison and Maximum Likelihood.  ...  Motivation: Word-based or 'alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate.  ...  In addition to these difficulties, exact algorithms for character-based phylogeny approaches are themselves NP hard [11, 21] .  ... 
arXiv:1803.09222v2 fatcat:ucsh6iizjndojewwnuvkapzj5e

Invariant based quartet puzzling

Joseph P Rusinko, Brian Hipp
2012 Algorithms for Molecular Biology  
In 1987 Cavender and Felsenstein [4], Lake [5] , and Evans and Speed [6] introduced a new class of reconstruction algorithms based on invariants.  ...  Results: We found that our algorithm outperforms Maximum Likelihood based quartet puzzling on data sets simulated with low to medium evolutionary rates.  ...  The majority of existing algorithms for phylogenetic reconstruction fall into one of three classes: distance based algorithms, parsimony algorithms, and maximum likelihood based algorithms.  ... 
doi:10.1186/1748-7188-7-35 pmid:23217018 pmcid:PMC3549829 fatcat:fvlpd7vq5na3xdpdhekayrt6g4

Are Automatic Methods for Cognate Detection Good Enough for Phylogenetic Reconstruction in Historical Linguistics? [article]

Taraka Rama, Johann-Mattis List, Johannes Wahle, Gerhard Jäger
2018 arXiv   pre-print
Especially where scholars are merely interested in exploring the bigger picture of a language family's phylogeny, algorithms for automatic cognate detection are a useful complement for current research  ...  on language phylogenies.  ...  and Tiago Tresoldi for helping with Pama-Nyungan data, Paul Sidwell for helping with Austro-Asiatic data, as well as the audience at the CESC 2017 conference (MPI-SHH, Jena) for their helpful comments on  ... 
arXiv:1804.05416v1 fatcat:3bituayf6jaffctxtgzxbvry4e
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