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Approximation Algorithms for the Fixed-Topology Phylogenetic Number Problem

M. Cryan L. A. Goldberg, C. A. Phillips
1999 Algorithmica  
We consider the fixed-topology version of this problem for fixed-topologies of arbitrary degree. This version of the problem is known to be A?  ...  Our 2-approximation algorithm is the first application of linear programming to approximation algorithms for phylogeny problems.  ...  The remainder of our paper is organized as follows: in section 2, we give the 2-approximation 2. A 2-approximation algorithm for the fixed-topology phylogenetic number problem.  ... 
doi:10.1007/pl00008280 fatcat:b2quid4j2bhcjkrkdfqyau2k4m

Approximation algorithms for the fixed-topology phylogenetic number problem [chapter]

Mary Cryan, Leslie Ann Goldberg, Cynthia A. Phillips
1997 Lecture Notes in Computer Science  
We consider the fixed-topology version of this problem for fixed-topologies of arbitrary degree. This version of the problem is known to be A?  ...  Our 2-approximation algorithm is the first application of linear programming to approximation algorithms for phylogeny problems.  ...  The remainder of our paper is organized as follows: in section 2, we give the 2-approximation 2. A 2-approximation algorithm for the fixed-topology phylogenetic number problem.  ... 
doi:10.1007/3-540-63220-4_56 fatcat:5nluwbon3natdey7n7ctkecrmy

Using genetic algorithms for the construction of phylogenetic trees: application to G-protein coupled receptor sequences

T.H Reijmers, R Wehrens, F.D Daeyaert, P.J Lewi, L.M.C Buydens
1999 Biosystems (Amsterdam. Print)  
In this article, genetic algorithms are applied such that the optimal tree can be found even with a bad initial tree topology.  ...  Many different phylogenetic clustering techniques are used currently.  ...  For a given distance matrix, the topology of the tree is fixed after applying a clustering method.  ... 
doi:10.1016/s0303-2647(98)00033-1 pmid:10091971 fatcat:qaz7hsceqfhcxf22tmmgo3bxra

Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks

Jaroslaw Byrka, Pawel Gawrychowski, Katharina T. Huber, Steven Kelk
2010 Journal of Discrete Algorithms  
algorithms that achieve approximation ratio better than p.  ...  For level-2 phylogenetic networks we show that p 0.61.  ...  Acknowledgements We thank Leo van Iersel and Jesper Jansson for very helpful comments.  ... 
doi:10.1016/j.jda.2009.01.004 fatcat:lmdavjhntfhs3df5yvr4xlvxoq

Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics [article]

Mathieu Fourment, Aaron E. Darling
2019 bioRxiv   pre-print
for phylogenetic inference.  ...  In this work, we explore the use of the Stan language for probabilistic programming in application to phylogenetic models.  ...  Acknowledgments We would like to thank Erick Matsen, Alexei Drummond, Christiaan Swanepoel and Cheng Zhang for useful discussions.  ... 
doi:10.1101/702944 fatcat:fpscrc2txnbihppcmpjj6btnve

Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks [article]

Jaroslaw Byrka, Pawel Gawrychowski, Katharina T. Huber, Steven Kelk
2008 arXiv   pre-print
We demonstrate the power of this result for the field of phylogenetics by giving worst-case optimal algorithms for level-1 phylogenetic networks (a much-studied extension of phylogenetic trees), improving  ...  For a given subclass of phylogenetic networks, what is the maximum value of 0 <= p <= 1 such that for every input set T of rooted triplets, there exists some network N(T) from the subclass such that at  ...  With the above construction we have shown that the existence of an ǫ-approximation algorithm for the MAX-LEVEL-0 problem implies existence of an ǫ-approximation algorithm for the MAX-IMUM SUBDAG problem  ... 
arXiv:0710.3258v3 fatcat:bsbaxt2ewzajbfeyqpyx6373ga

Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics

Mathieu Fourment, Aaron E. Darling
2019 PeerJ  
for phylogenetic inference.  ...  In this work, we explore the use of the Stan language for probabilistic programming in application to phylogenetic models.  ...  ACKNOWLEDGEMENTS We would like to thank Erick Matsen, Alexei Drummond, Christiaan Swanepoel and Cheng Zhang for useful discussions.  ... 
doi:10.7717/peerj.8272 pmid:31976168 pmcid:PMC6966998 fatcat:bqrzi5nhgraf3nthu7dg4u7tdm

A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem [chapter]

Gang Wu, Jia-Huai You, Guohui Lin
2005 Lecture Notes in Computer Science  
The branch-and-bound algorithm integrates a number of previous efforts on exact algorithms, heuristics, and approximation algorithms for the MQC problem, and a few improved search techniques, especially  ...  A lookahead branch-and-bound algorithm is proposed for solving the Maximum Quartet Consistency Problem where the input is a complete set of quartets on the taxa and the goal is to construct a phylogeny  ...  To get good bounds for speedup in our branch-and-bound algorithm, we review in the following a few heuristics and approximation algorithms that have been designed for the MQC problem and/or the MQI problem  ... 
doi:10.1007/11557067_6 fatcat:4oaadvuafvhtnlguzyxgopmrbm

Probabilistic Path Hamiltonian Monte Carlo [article]

Vu Dinh, Arman Bilge, Cheng Zhang, Frederick A. Matsen IV
2017 arXiv   pre-print
, this rather complex space is not suitable for existing HMC algorithms.  ...  We define PPHMC on orthant complexes, show that the resulting Markov chain is ergodic, and provide a promising implementation for the case of phylogenetic trees in open-source software.  ...  Second, starting with the current augmented state, s = (τ, q, p), the Hamiltonian dynamics is run for a fixed number of steps T using the leap-prog algorithm with fixed step size .  ... 
arXiv:1702.07814v2 fatcat:sy2suqdaafapbekib7nmtzd7yu

An ant colony optimization algorithm for phylogenetic estimation under the minimum evolution principle

Daniele Catanzaro, Raffaele Pesenti, Michel C Milinkovitch
2007 BMC Evolutionary Biology  
This is the first application of an ACO algorithm to the phylogenetic estimation problem.  ...  This behavior is exploited in artificial ant colonies for the search of approximate solutions to discrete optimization problems.  ...  This work was supported by the "Communauté Française de Belgique" (ARC 11649/20022770) and the "Région Wallone". We thank C. Korostensky, and Mike Steel for helpful discussions, as well as J. L.  ... 
doi:10.1186/1471-2148-7-228 pmid:18005416 pmcid:PMC2211314 fatcat:3mtrzm5ejvepnascq3rwphfdh4

Page 5978 of Mathematical Reviews Vol. , Issue 2000h [page]

2000 Mathematical Reviews  
[Phillips, Cynthia A.] (1-SAND; Albuquerque, NM) Approximation algorithms for the fixed-topology phylogenetic number problem. (English summary) Algorithmica 25 (1999), no. 2-3, 311-329.  ...  The authors of the present paper use linear programming techniques to provide a 2-approximation algorithm for this problem for all 1 > 3.  ... 

PBPI: a High Performance Implementation of Bayesian Phylogenetic Inference

Xizhou Feng, Kirk Cameron, Duncan Buell
2006 ACM/IEEE SC 2006 Conference (SC'06)  
PBPI also achieves linear speedup with the number of processors for large problem sizes.  ...  This paper describes the implementation and performance of PBPI, a parallel implementation of Bayesian phylogenetic inference method for DNA sequence data.  ...  This implementation of MrBayes increases the number of chains to effectively scale the work load while fixing the problem size.  ... 
doi:10.1109/sc.2006.47 fatcat:4hihqgsl3rdaddl676syatmfbu

Heuristic Algorithms for the Protein Model Assignment Problem [chapter]

Jörg Hauser, Kassian Kobert, Fernando Izquierdo-Carrasco, Karen Meusemann, Bernhard Misof, Michael Gertz, Alexandros Stamatakis
2013 Lecture Notes in Computer Science  
We show that our heuristics can find PMAs with better log likelihood scores on a fixed, reasonable tree topology than the naïve approach to the PMA, which ignores the fact that branch lengths are linked  ...  Given p partitions and the approximately 20 empirical protein models that are available, one needs to compute the log likelihood score of 20 p possible model-to-partition assignments for obtaining the  ...  For all 15 test datasets, we were able to find a PMA with a better likelihood than obtained via the naïve algorithm on the the same, fixed, reasonable tree topology.  ... 
doi:10.1007/978-3-642-38036-5_16 fatcat:zmwtmgtcn5gzdanwll3zaelida

From a Phylogenetic Tree to a Reticulated Network

Vladimir Makarenkov, Pierre Legendre
2004 Journal of Computational Biology  
The algorithm produces a reticulate phylogeny by gradually improving upon the initial solution provided by a phylogenetic tree model.  ...  In many phylogenetic problems, assuming that species have evolved from a common ancestor by a simple branching process is unrealistic.  ...  Yves Desdevises for help during the phylogenetic analyses.  ... 
doi:10.1089/106652704773416966 pmid:15072696 fatcat:el7h34hsvvhchdpdiwc6auiggm

Page 7843 of Mathematical Reviews Vol. , Issue 2002K [page]

2002 Mathematical Reviews  
The related problem of finding a maximum subgraph of a fixed diameter d > | is proved to be even harder to approximate.”  ...  {For the entire collection see MR 2002h:05002. } 2002k:05227 05C85 05C69 Shaheen, Ramy S. (SY-TISHS; Lattakia) Algorithm for computing the domination number of graphs.  ... 
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