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Applications and Algorithms for Inference of Huge Phylogenetic Trees: a Review

Muhammad Sardaraz, Muhammad Tahir, Tahir Aziz Ikram, Hassan Bajwa
2012 American Journal of Bioinformatics Research  
the inference of phylogenetic trees.  ...  This article presents a comprehensive survey of the applications and the algorithms for inference of huge phylogenetic trees and also gives the reader an overview of the methods currently employed for  ...  Inference of the phylogeny is based on the posterior probabilities of the phylogenetic trees.  ... 
doi:10.5923/j.bioinformatics.20120201.04 fatcat:cwskdp7b6ze6xdlq5qekgypjwm

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics

Raphaël Helaers, Michel C Milinkovitch
2010 BMC Bioinformatics  
Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such  ...  The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences  ...  of the manuscript.  ... 
doi:10.1186/1471-2105-11-379 pmid:20633263 pmcid:PMC2912891 fatcat:d3h6oej2srhvdd35h4femd6wse

A generic and versatile architecture for inference of evolutionary trees under maximum likelihood

Nikolaos Alachiotis, Alexandros Stamatakis
2010 2010 Conference Record of the Forty Fourth Asilomar Conference on Signals, Systems and Computers  
We propose a dedicated computer architecture for the inference of phylogenies under the maximum likelihood criterion.  ...  It can also optimize the branch lengths of tree topologies and calculate transition probability matrices. We used FPGA technology to verify the correctness of our architecture.  ...  Hence the PLF as used in Bayesian inference programs is less complex than for ML programs.  ... 
doi:10.1109/acssc.2010.5757682 fatcat:egyxtb3xznf5hm3firi3cdw4wy

FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

Stephanie Zierke, Jason D Bakos
2010 BMC Bioinformatics  
FPGAs in particular are well-suited for this task because of their low power consumption as compared to many-core processors and Graphics Processor Units (GPUs) [1] .  ...  By leveraging the FPGA's on-chip DSP modules and the high-bandwidth local memory attached to the FPGA, the resultant co-processor can accelerate ML-based methods and outperform state-of-the-art multi-core  ...  Acknowledgements We thank the anonymous reviewers whose comments have led to substantial improvements to this paper.  ... 
doi:10.1186/1471-2105-11-184 pmid:20385005 pmcid:PMC2868009 fatcat:dxsk3bsn7rcxtpqqb4jexl5fbi

chromploid: An R package for chromosome number evolution across the plant tree of life

Rosana Zenil-Ferguson, J. Gordon Burleigh, José Miguel Ponciano
2018 Applications in Plant Sciences  
CONCLUSIONS: chromploid enables researchers to perform robust likelihood-based inferences using complex models of chromosome number evolution across large phylogenies.  ...  We introduce the R package chromploid, which allows scientists to perform inference of chromosomal evolution rates across large phylogenetic trees.  ...  Harmon for insightful comments on this manuscript and Dr. Emma Goldberg for insights about the Solanum data set. R.Z.F. was supported by the National Science Foundation (NSF; grant no.  ... 
doi:10.1002/aps3.1037 pmid:29732267 pmcid:PMC5895187 fatcat:7nhiaemcnjgppbasype3xh4qmy

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

Sebastian Höhna, Michael J. Landis, Tracy A. Heath, Bastien Boussau, Nicolas Lartillot, Brian R. Moore, John P. Huelsenbeck, Fredrik Ronquist
2016 Systematic Biology  
Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models.  ...  [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.] Academy Course entitled "Phylogenetic analysis using RevBayes".  ...  ACKNOWLEDGMENTS The authors wish to thank the National Evolutionary Synthesis Center (NESCent) for sponsoring the NESCent  ... 
doi:10.1093/sysbio/syw021 pmid:27235697 pmcid:PMC4911942 fatcat:ikjyrejb2bfntgdgqvlvomukpe

Phylogenetics [chapter]

Eliane Barbosa Evanovich dos Santos
2018 Phylogenetics [Working Title]  
parsimony, neighbor joining, UPGMA, maximum likelihood, and Bayesian inference.  ...  This view, although prior to Charles Darwin, only gained deserved prominence after On the Origin of Species.  ...  Bayesian inference As the maximum likelihood, the Bayesian inference is also a probabilistic method.  ... 
doi:10.5772/intechopen.79422 fatcat:kxujyjf7gre67hugorj34lcazi

Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction [article]

Mandev S. Gill, Philippe Lemey, Marc A. Suchard, Andrew Rambaut, Guy Baele
2020 arXiv   pre-print
Our procedure is implemented in the BEAST 1.10 software package, and relies on a distance-based measure to insert new taxa into the current estimate of the phylogeny and imputes plausible values for new  ...  Widely-used Bayesian phylogenetic inference packages are not set up for this purpose, generally requiring one to recompute trees and evolutionary model parameters de novo when new data arrive.  ...  Our online inference approach leads to higher computation time savings as the complexity of the data increases, with up to 600 hours being saved on average on a modern multi-core processor.  ... 
arXiv:2002.00245v1 fatcat:yeugmktxsnaljdbx7psyvewfbi

Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction

2020 Molecular biology and evolution  
Our procedure is implemented in the BEAST 1.10 software package, and relies on a distance-based measure to insert new taxa into the current estimate of the phylogeny and imputes plausible values for new  ...  Widely-used Bayesian phylogenetic inference packages are not set up for this purpose, generally requiring one to recompute trees and evolutionary model parameters de novo when new data arrive.  ...  The research leading to these results has received funding from the European Research The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center  ... 
doi:10.1093/molbev/msaa047 pmid:32101295 pmcid:PMC7253210 fatcat:xxgy5g4exrfxnm5nvettm77mo4

Efficient Implementation of MrBayes on Multi-GPU

J. Bao, H. Xia, J. Zhou, X. Liu, G. Wang
2013 Molecular biology and evolution  
As a leading method of using DNA data to infer phylogeny, the (MC) 3 Bayesian algorithm and its improved and parallel versions are now not fast enough for biologists to analyze massive real-world DNA data  ...  Recently, graphics processor unit (GPU) has shown its power as a coprocessor (or rather, an accelerator) in many fields.  ...  Acknowledgments This work was partially supported by National Natural Science Foundation of China (grant numbers 60903028 and 61070014) and by Key Projects in the Tianjin Science & Technology Pillar Program  ... 
doi:10.1093/molbev/mst043 pmid:23493260 pmcid:PMC3649675 fatcat:q3qs3dnsardcznob5rect276fa

Stepwise Bayesian Phylogenetic Inference [article]

Sebastian Hoehna, Allison Yi Hsiang
2020 bioRxiv   pre-print
The ideal approach to Bayesian phylogenetic inference is to estimate all parameters of interest jointly in a single hierarchical model.  ...  Here, we formally develop and test the stepwise approach to Bayesian inference, which uses importance sampling to generate observations for the next step of an analysis pipeline from the posterior produced  ...  We also want to thank Jiansi Gao for his insights into the stepwise Bayesian approach employed in BEAST.  ... 
doi:10.1101/2020.11.11.376459 fatcat:u2mtezzkgngwta6hbzuelbf3py

High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE [chapter]

Guy Baele, Daniel L. Ayres, Andrew Rambaut, Marc A. Suchard, Philippe Lemey
2019 Msphere  
packages for both Bayesian inference and maximum-likelihood frameworks.  ...  CPUs) and a wide range of graphics processing cards (GPUs).  ...  We gratefully acknowledge support from the NVIDIA Corporation with the donation of parallel computing resources used for this research.  ... 
doi:10.1007/978-1-4939-9074-0_23 pmid:31278682 fatcat:bwskcq5cd5bptggagce2cp7toa

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  
Single precision requires more frequent use of a rescaling scheme to avoid underflow but allows BEAGLE to run on a greater variety of graphics processors since initial generations of such hardware did  ...  such as Bayesian inference and maximum likelihood estimation.  ... 
doi:10.1093/sysbio/syr100 pmid:21963610 pmcid:PMC3243739 fatcat:yjhr75hwdbdjvpeid65opwag2a

PALM: A Paralleled and Integrated Framework for Phylogenetic Inference with Automatic Likelihood Model Selectors

Shu-Hwa Chen, Sheng-Yao Su, Chen-Zen Lo, Kuei-Hsien Chen, Teng-Jay Huang, Bo-Han Kuo, Chung-Yen Lin, Magnus Rattray
2009 PLoS ONE  
PALM results in an inference of phylogenetic relationship not only by vanquishing the computation difficulty of ML methods but also providing statistic methods for model selection and bootstrapping.  ...  To accelerate the computing of maximum likelihood and bootstrapping, this work integrates MPICH2/ PhyML, PalmMonitor and Palm job controller across several machines with multiple processors and adopts  ...  Acknowledgments The authors would like to thank Dr. Stephane Guindon for invaluable suggestions and efforts in refining the mpi of PhyML. Appreciation is also extended to the teams lead by Dr.  ... 
doi:10.1371/journal.pone.0008116 pmid:19997614 pmcid:PMC2785425 fatcat:et6h2ktq4bgvrlloht3nimky3u

OUP accepted manuscript

2019 Molecular biology and evolution  
We focus on best practices, potential pitfalls, and recommendations that can be generalized to other software packages for Bayesian inference.  ...  We here provide a practical guide to using BEAST and its accompanying applications for the purpose of drawing inference under these models.  ...  Bayesian inference setup.  ... 
doi:10.1093/molbev/msz172 fatcat:h2yvt4dc5ncg3ltyi6ezkrwyee
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