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Approximation Algorithms for the Fixed-Topology Phylogenetic Number Problem

1999
*
Algorithmica
*

We consider

doi:10.1007/pl00008280
fatcat:b2quid4j2bhcjkrkdfqyau2k4m
*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*. ...##
###
Approximation algorithms for the fixed-topology phylogenetic number problem
[chapter]

1997
*
Lecture Notes in Computer Science
*

We consider

doi:10.1007/3-540-63220-4_56
fatcat:5nluwbon3natdey7n7ctkecrmy
*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*. ...##
###
Using genetic algorithms for the construction of phylogenetic trees: application to G-protein coupled receptor sequences

1999
*
Biosystems (Amsterdam. Print)
*

In this article, genetic

doi:10.1016/s0303-2647(98)00033-1
pmid:10091971
fatcat:qaz7hsceqfhcxf22tmmgo3bxra
*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. ...##
###
Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks

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. ...

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

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. ...

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

2008
*
arXiv
*
pre-print

We demonstrate

arXiv:0710.3258v3
fatcat:bsbaxt2ewzajbfeyqpyx6373ga
*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*...##
###
Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics

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. ...

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

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*...

##
###
Probabilistic Path Hamiltonian Monte Carlo
[article]

2017
*
arXiv
*
pre-print

, this rather complex space is not suitable

arXiv:1702.07814v2
fatcat:sy2suqdaafapbekib7nmtzd7yu
*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 . ...##
###
An ant colony optimization algorithm for phylogenetic estimation under the minimum evolution principle

2007
*
BMC Evolutionary Biology
*

This is

doi:10.1186/1471-2148-7-228
pmid:18005416
pmcid:PMC2211314
fatcat:3mtrzm5ejvepnascq3rwphfdh4
*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. ...##
###
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

2006
*
ACM/IEEE SC 2006 Conference (SC'06)
*

PBPI also achieves linear speedup with

doi:10.1109/sc.2006.47
fatcat:4hihqgsl3rdaddl676syatmfbu
*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. ...##
###
Heuristic Algorithms for the Protein Model Assignment Problem
[chapter]

2013
*
Lecture Notes in Computer Science
*

We show that our heuristics can find PMAs with better log likelihood scores on a

doi:10.1007/978-3-642-38036-5_16
fatcat:zmwtmgtcn5gzdanwll3zaelida
*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*. ...##
###
From a Phylogenetic Tree to a Reticulated Network

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. ...

##
###
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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