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New Approaches to Compare Phylogenetic Search Heuristics

Seung-Jin Sul, Suzanne Matthews, Tiffani L. Williams
2008 2008 IEEE International Conference on Bioinformatics and Biomedicine  
Thus, by understanding phylogenetic heuristic behavior, better heuristics could be designed, which ultimately leads to more accurate evolutionary trees.  ...  Secondly, we develop a new entropybased measure to quantify the diversity among the evolutionary trees found by the heuristics.  ...  This new starting tree is then used with the original data set to repeat the phylogenetic search.  ... 
doi:10.1109/bibm.2008.81 dblp:conf/bibm/SulMW08 fatcat:glp55o3dtrh23dwfalefjdusbq

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

R. Lanfear, B. Calcott, S. Y. W. Ho, S. Guindon
2012 Molecular biology and evolution  
These methods allow millions of partitioning schemes to be compared in realistic time frames and so permit the objective selection of partitioning schemes even for large multilocus DNA data sets.  ...  We hope that PartitionFinder will encourage the objective selection of partitioning schemes and thus lead to improvements in phylogenetic analyses.  ...  Comparing Exhaustive and Heuristic Searches in PartitionFinder We tested the ability of our heuristic algorithm to find optimal partitioning schemes for ten data sets obtained from Data Dryad (www.datadryad.org  ... 
doi:10.1093/molbev/mss020 pmid:22319168 fatcat:jvj7qdxnunc5jpxmptxe235yle

Large-Scale Analysis of Phylogenetic Search Behavior [chapter]

Hyun Jung Park, Seung-Jin Sul, Tiffani L. Williams
2010 Advances in Experimental Medicine and Biology  
Most analyses rely on effective heuristics for obtaining accurate trees. However, relatively little work has been done to analyze quantitatively the behavior of phylogenetic heuristics in tree space.  ...  A better understanding of local search behavior can facilitate the design of better heuristics, which ultimately lead to more accurate depictions of the true evolutionary relationships.  ...  Acknowledgements The authors wish to thank Bill Murphy and Matt Yoder for providing us with the biological datasets used in this study.  ... 
doi:10.1007/978-1-4419-5913-3_5 pmid:20865484 fatcat:yu5jqegkmzfhvpwctk2we2pise

Using tree diversity to compare phylogenetic heuristics

Seung-Jin Sul, Suzanne Matthews, Tiffani L Williams
2009 BMC Bioinformatics  
We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms.  ...  Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space.  ...  Thus, the most popular techniques in the field use heuristics to reconstruct phylogenetic trees. In this paper, we develop new techniques to compare the performance of phylogenetic heuristics.  ... 
doi:10.1186/1471-2105-10-s4-s3 pmid:19426451 pmcid:PMC2681068 fatcat:ytp6f27bzzghfpl4k6p3awsnae

The role of diverse populations in phylogenetic analysis

Tiffani L. Williams, Marc L. Smith
2006 Proceedings of the 8th annual conference on Genetic and evolutionary computation - GECCO '06  
The most popular approaches for reconstructing phylogenetic trees attempt to solve NP-hard optimization criteria such as maximum parsimony (MP).  ...  We compare the performance of Cooperative Rec-I-DCM3 to Rec-I-DCM3 on four large biological datasets.  ...  Unfortunately, the performance of these genetic algorithms are often not compared to the top performing phylogenetic heuristics.  ... 
doi:10.1145/1143997.1144046 dblp:conf/gecco/WilliamsS06 fatcat:qrckiiww6vcsnla5cqp2eyu3ku

Phylogenetic Hypotheses and the Utility of Multiple Sequence Alignment [chapter]

Ward C. Wheeler, Gonzalo Giribet
2009 Sequence AlignmentMethods, Models, Concepts, and Strategies  
As far as these simulations are concerned, the one-step heuristic approach of POY is overwhelmingly superior to that of the two step alignment + tree search approach advocated by Ogden and Rosenberg (  ...  A phylogenetic search seeks to minimize the TAP cost over the universe of possible trees.  ... 
doi:10.1525/california/9780520256972.003.0006 fatcat:jwdkd5swqvew7gm42uhu4srmxy

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

A. Wehe, M. S. Bansal, J. G. Burleigh, O. Eulenstein
2008 Bioinformatics  
The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses  ...  DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach.  ...  Funding: National Science Foundation (EF-0334832 to A.W., M.S.B. and O.E., and EF-0423641 to J.G.B.). Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btn230 pmid:18474508 fatcat:2vinmtq4i5ftnntijbr5b4cssa

Pylogeny: an open-source Python framework for phylogenetic tree reconstruction and search space heuristics

Alexander Safatli, Christian Blouin
2015 PeerJ Computer Science  
Its primary function is to permit both heuristic search and analysis of the phylogenetic tree search space, as well as to enable the design of novel algorithms to search this space.  ...  Pylogeny is a cross-platform library for the Python programming language that provides an object-oriented application programming interface for phylogenetic heuristic searches.  ...  As an example, one could perform a greedy hill-climbing heuristic on the search space by comparing the trees' parsimony scores.  ... 
doi:10.7717/peerj-cs.9 fatcat:drkgyn23ejgpvc3k7fatbeealy

Fast NeighborNet: Improving the Speed of the Neighbor-Net Phylogenetic Network Algorithm with Multithreading and a Relaxed Search Strategy [article]

Jacob Porter
2018 bioRxiv   pre-print
Fast Neighbor-Net is a command-line Java program that has fast implementations of the popular Neighbor-Net phylogenetic split network approach.  ...  These search strategies allow multithreading to better use modern CPU hardware. PFAM data of 2000--30,000 taxa were used for testing performance.  ...  Another algorithm that computes phylogenetic split networks is split decomposition [1] , but networks may not be planar and may be less resolved compared to Neighbor-Net [11] .  ... 
doi:10.1101/283424 fatcat:jsl3bjulsfcrhouhua24rkbwpy

Trees from Trees: Construction of Phylogenetic Supertrees Using Clann [chapter]

Christopher J. Creevey, James O. McInerney
2009 Msphere  
Some of the longest standing phylogenetic conundrums are now being brought to light using supertree approaches.  ...  Supertree methods combine multiple phylogenetic trees to produce the overall best "supertree".  ...  If this is done during the random sampling phase of a heuristic search, it will allow the user to move straight to the heuristic search without completing the random sampling. 9 .  ... 
doi:10.1007/978-1-59745-251-9_7 pmid:19378143 fatcat:iib2alwuzreiddxhmmm2xpj3ki

An open source phylogenetic search and alignment package

Hyrum Carroll, Adam R. Teichert, Jonathan Krein, Kenneth Sundberg, Quinn Snell, Mark Clement
2009 International Journal of Bioinformatics Research and Applications  
PSODA offers performance comparable to PAUP* in an open source package that aims to provide a foundation for researchers examining new phylogenetic algorithms.  ...  A key new feature is PsodaScript, an extension to the nearly ubiquitous NEXUS format, that includes conditional and loop constructs; thereby allowing complex meta-search techniques like the parsimony ratchet  ...  Acknowledgements We would like to thank the beta testers of PSODA for their insightful comments.  ... 
doi:10.1504/ijbra.2009.026424 pmid:19525205 fatcat:zmary2oxy5hjpi7voctlgumpsy

Phylospaces: reconstructing evolutionary trees in tuple space

M.L. Smith, T.L. Williams
2006 Proceedings 20th IEEE International Parallel & Distributed Processing Symposium  
We compare the performance of the algorithms on two datasets consisting of 2,000 and 7,769 taxa, respectively.  ...  We use Phylospaces to devise Cooperative Rec-I-DCM3, a population-based strategy for navigating tree space.  ...  The authors would also like to thank Usman Roshan for providing the code for Rec-I-DCM3 and the datasets to use for this study.  ... 
doi:10.1109/ipdps.2006.1639533 dblp:conf/ipps/SmithW06 fatcat:jdmr3dceczhvlptpoiaj3egpxi

A heuristic approach of maximum likelihood method for inferring phylogenetic tree and an application to the mammalianSOX-3origin of the testis-determining geneSRY

Kazutaka Katoh, Takashi Miyata
1999 FEBS Letters  
Applying the tree bisection and reconnection (TBR) algorithm, we have developed a heuristic method (maximum likelihood (ML)-TBR) for inferring the ML tree based on tree topology search.  ...  This method has been applied to the inference of phylogenetic tree of the SOX family members.  ...  The heuristic approach is further extended in this paper by applying a more sophisticated topology search algorithm, the tree bisection and reconnection (TBR) method [9] , and the new method is applied  ... 
doi:10.1016/s0014-5793(99)01621-x pmid:10601652 fatcat:hlnugukqhnfejpzfzqe5ga73ri

Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

Yun Yu, R. Matthew Barnett, Luay Nakhleh
2013 Systematic Biology  
To address this issue, we present a parsimony criterion for reconciling gene trees within the branches of a phylogenetic network, and a local search heuristic for inferring phylogenetic networks from collections  ...  A phylogenetic approach to detect hybridization entails sequencing multiple loci across the genomes of a group of species of interest, reconstructing their gene trees, and taking their differences as indicators  ...  Sloan Research Fellowship, and a Guggenheim Fellowship (to L.N.).  ... 
doi:10.1093/sysbio/syt037 pmid:23736104 pmcid:PMC3739885 fatcat:lfjxwd22kjcnrarffoozzommhy

A novel approach to phylogenetic trees:d-Dimensional geometric Steiner trees

M. Brazil, D.A. Thomas, B.K. Nielsen, P. Winter, C. Wulff-Nilsen, M. Zachariasen
2009 Networks  
Experiments also indicate that the new method is comparable with results produced by Neighbor Joining [20] .  ...  Preliminary computational experience shows that the use of Euclidean Steiner trees for finding phylogenetic trees is a viable approach.  ...  For this paper we have designed a simple Steiner tree heuristic to evaluate our general approach to computing phylogenetic trees.  ... 
doi:10.1002/net.20279 fatcat:phj2lobpy5hdncoaicf7wgzmji
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