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GPU MrBayes V3.1: MrBayes on Graphics Processing Units for Protein Sequence Data: Table 1

Shuai Pang, Rebecca J. Stones, Ming-Ming Ren, Xiao-Guang Liu, Gang Wang, Hong-ju Xia, Hao-Yang Wu, Yang Liu, Qiang Xie
2015 Molecular biology and evolution  
We present a modified GPU (graphics processing unit) version of MrBayes, called ta(MC) 3 (GPU MrBayes V3.1), for Bayesian phylogenetic inference on protein data sets.  ...  Versus the current fastest software, we achieve a speedup of up to around 2.5 (and up to around 90 vs. serial MrBayes), and more on multi-GPU hardware.  ...  To further test the capabilities of ta(MC) 3 , we run it on a GPU cluster on the Tianhe-1 A supercomputer.  ... 
doi:10.1093/molbev/msv129 pmid:26012905 fatcat:mwy7ceczhzfzhe5fuaj27mjboq

A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library

Fernando Izquierdo-Carrasco, Nikolaos Alachiotis, Simon Berger, Tomas Flouri, Solon P. Pissis, Alexandros Stamatakis
2013 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum  
We compare the performance of our GPU implementation for DNA data with a highly optimized x86 version of the PLL that relies on manually tuned AVX intrinsics.  ...  We conclude that, a hybrid GPU-CPU version needs to be developed and integrated into the PLL to leverage the computational power of modern desktop systems and clusters.  ...  With respect to future work, we plan to fully integrate the GPU kernel with the PLL and support all models and data types (e.g., protein data and the CAT model of rate heterogeneity).  ... 
doi:10.1109/ipdpsw.2013.103 dblp:conf/ipps/Izquierdo-CarrascoABFPS13 fatcat:shracbwghfg77kfvefvdoxvbp4

Novel Detection of Insecticide Resistance Related P450 Genes and Transcriptome Analysis of the Hemimetabolous Pest Erthesina fullo (Thunberg) (Hemiptera: Heteroptera)

Yang Liu, Haoyang Wu, Qiang Xie, Wenjun Bu, Youjun Zhang
2015 PLoS ONE  
We reported a de novo assembled and annotated transcriptome for adult E. fullo using the Illumina sequence system.  ...  sequences and analyzed the evolution of cytochrome P450 superfamilies, genes of the CYP3 clan related to metabolizing xenobiotics and plant natural compounds, in E. fullo, increasing the candidate genes for  ...  Acknowledgments The authors thank the technical staff in the College of Computer and Control Engineering (Nankai University) for their help in some bioinformatics analysis.  ... 
doi:10.1371/journal.pone.0125970 pmid:25955554 pmcid:PMC4425472 fatcat:op46kgue55fl7lt7rszkrmuagy

A reference guide for tree analysis and visualization

Georgios A Pavlopoulos, Theodoros G Soldatos, Adriano Barbosa-Silva, Reinhard Schneider
2010 BioData Mining  
For example, the current phylogenetic tree visualization tools are not able to display easy to understand large scale trees with more than a few thousand nodes.  ...  Clustering analysis is becoming more and more difficult to be applied on very large amounts of data since the results of these algorithms cannot be efficiently visualized.  ...  For example, one can generate a phylogenetic tree from protein sequence alignment data using parsimony criteria, generate a pairwise sequence distance matrix based on an alignment of protein sequences,  ... 
doi:10.1186/1756-0381-3-1 pmid:20175922 pmcid:PMC2844399 fatcat:k2k6u72nandljivhdbxvstuy2u

Deep residual neural networks resolve quartet molecular phylogenies [article]

Zhengting Zou, Hongjiu Zhang, Yuanfang Guan, Jianzhi George Zhang
2019 bioRxiv   pre-print
We train residual networks on simulated protein sequence data with extensive amino acid substitution heterogeneities.  ...  Phylogenetic inference is of fundamental importance to evolutionary as well as other fields of biology, and molecular sequences have emerged as the primary data for this task.  ...  We thank the support of NVIDIA Corporation with the donation of the Titan Xp GPU used in this research.  ... 
doi:10.1101/787168 fatcat:23v2bcvm4felhjt55seytvmhse

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  
We discuss computational improvements brought about by the BEAGLE library on a variety of state-of-the-art multicore hardware, and for a range of commonly used evolutionary models.  ...  In conclusion, we show that for increasingly large molecular sequence data sets, GPUs can offer tremendous computational advancements through the use of the BEAGLE library, which is available for software  ...  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

Variational Combinatorial Sequential Monte Carlo Methods for Bayesian Phylogenetic Inference [article]

Antonio Khalil Moretti, Liyi Zhang, Christian A. Naesseth, Hadiah Venner, David Blei, Itsik Pe'er
2021 arXiv   pre-print
Bayesian phylogenetic inference is often conducted via local or sequential search over topologies and branch lengths using algorithms such as random-walk Markov chain Monte Carlo (MCMC) or Combinatorial  ...  We show that VCSMC and VNCSMC are computationally efficient and explore higher probability spaces than existing methods on a range of tasks.  ...  Acknowledgements We thank the reviewers for their helpful feedback. We acknowledge funding from NIH/NCI grant U54CA209997 and two NIH shared instrumentation grants, S10 OD012351 and S10 OD021764.  ... 
arXiv:2106.00075v2 fatcat:jnz5etloqzawxfcaqm5cwswvfq

Efficient Computation of the Phylogenetic Likelihood Function on the Intel MIC Architecture

Alexey M. Kozlov, Christian Goll, Alexandros Stamatakis
2014 2014 IEEE International Parallel & Distributed Processing Symposium Workshops  
Phylogenetic inference is the process of reconstructing the evolutionary history of species based on their traits, nowadays mostly using molecular sequence data.  ...  Using a MIC-based accelerator (Xeon Phi 5110P), we were able to achieve speedups ranging from 1.9x to 2.8x for different PLF kernels, compared to a highly optimized AVX implementation running on dual-socket  ...  Nowadays, most phylogenetic analyses use molecular traits, that is, DNA, RNA, or protein sequences.  ... 
doi:10.1109/ipdpsw.2014.198 dblp:conf/ipps/KozlovGS14 fatcat:vkbnfu7l3bfptmjmpqhfvca3im

Scalable Workflows and Reproducible Data Analysis for Genomics [chapter]

Francesco Strozzi, Roel Janssen, Ricardo Wurmus, Michael R. Crusoe, George Githinji, Paolo Di Tommaso, Dominique Belhachemi, Steffen Möller, Geert Smant, Joep de Ligt, Pjotr Prins
2019 Msphere  
Together these distributions represent the overall majority of software packages relevant for biology, including PAML, Muscle, MAFFT, MrBayes, and BLAST.  ...  Due to large volumes, the analysis and integration of data generated by such high-throughput technologies have become computationally intensive, and analysis can no longer happen on a typical desktop computer.In  ...  MrBayes, for example, a program for calculating phylogenetic trees based on Bayesian analysis, comes with MPI support.  ... 
doi:10.1007/978-1-4939-9074-0_24 pmid:31278683 fatcat:qtv5vvi2vjhkvaqp42cvqo5eh4

Archaea, the tree of life, and cellular evolution in eukaryotes

Jing Xiao, Lu Fan, Dingfeng Wu, Yanbing Xu, Dengxun Lai, William F. Martin, Ruixin Zhu, Chuanlun Zhang
2019 Science China. Earth Sciences  
We also highlight both the advantages and challenges brought by increasingly available metagenomic data on Archaea, data that have quickly moved to the forefront of the field.  ...  Here we give a brief review of the studies on Archaea, the tree of life and the cellular evolution of eukaryotes, which is followed by an overview of recent progress fueled by new genomic technologies  ...  Marine Geology, Qingdao National Laboratory for Marine Science and Technology (Grant No.  ... 
doi:10.1007/s11430-018-9326-1 fatcat:b2zylklnxvde3dorepeyh562vq

The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene

Anna V. Williams, Laura M. Boykin, Katharine A. Howell, Paul G. Nevill, Ian Small, Chih-Horng Kuo
2015 PLoS ONE  
Results and Discussion Sequencing and assembly Dried herbarium material of a specimen of Acacia ligulata Benth. was used for DNA extraction.  ...  In A. ligulata, although transcribed and spliced, it probably encodes a catalytically inactive protein.  ...  Acknowledgments Our thanks go to Hayden Walker for his aid with genome assembly, to Joe Miller for his advice on Acacia biology and phylogeny, and to Erik Koenen for providing the unpublished Inga leiocalycina  ... 
doi:10.1371/journal.pone.0125768 pmid:25955637 pmcid:PMC4425659 fatcat:micerd5bp5dpxo6ehvufzm5ndy

Origin and evolution of transporter substrate specificity within the NPF family

Morten Egevang Jørgensen, Deyang Xu, Christoph Crocoll, David Ramírez, Mohammed Saddik Motawia, Carl Erik Olsen, Hussam Hassan Nour-Eldin, Barbara Ann Halkier
2017 eLife  
Biochemical characterization of orthologs along the phylogenetic lineage from cassava to A. thaliana, suggests that alterations in the electrogenicity of the transporters accompanied changes in substrate  ...  Daniel J Kliebenstein are thanked for help with phylogenetic analyses, critical reading and constructive comments on the manuscript. Technician Anja Hecht Ivø and Assist. Prof.  ...  Kristian Holst Laursen are thanked for technical assistance with the IRMS analyses. Imaging data were collected at the Center for Advanced Bioimaging (CAB) Denmark, University of Copenhagen.  ... 
doi:10.7554/elife.19466 pmid:28257001 pmcid:PMC5336358 fatcat:p5youvxhsbh2fmmwtj35v7a6pu

The Complete Mitochondrial Genome of the Stalk-Eyed Bug Chauliops fallax Scott, and the Monophyly of Malcidae (Hemiptera: Heteroptera)

Teng Li, Cuiqing Gao, Ying Cui, Qiang Xie, Wenjun Bu, Patrick CY. Woo
2013 PLoS ONE  
A remarkable strand bias was found for all nine protein coding genes (PCGs) encoded by the majority strand were positive AT-skew and negative GC-skew, whereas the reverse were found in the remaining four  ...  Phylogenetic analyses were carried out based on all the 13 PCGs showed that Chauliopinae was the sister group of Malcinae and the monophyly of Lygaeoidea.  ...  Xiaoguang Liu and Gang Wang (College of Information Technical Science, Nankai University) for help with parallel running of the GPU MrBayes program.  ... 
doi:10.1371/journal.pone.0055381 pmid:23390534 pmcid:PMC3563593 fatcat:z4t4bigstbhbhnyllvetb2wjja

Molecular Phylogenetic Analysis: Design and Implementation of Scalable and Reliable Algorithms and Verification of Phylogenetic Properties

Jorge Álvarez-Jarreta, Gregorio De Miguel Casado, Elvira Mayordomo
1970 Jornada de Jóvenes Investigadores del I3A  
We here present several contributions we have published as solution for different problems involved in the study of the evolution process.  ...  MrBayes [96, 97] is one of the most used software tools as to the BI method.  ...  This suggests about one error per 10 proteins formed for a common length protein (≈ 300 amino acids) [39] .  ... 
doi:10.26754/jji-i3a.201701595 fatcat:22bgiopaufhtvd7sawp47p6zhq

Next Generation Distributed Computing for Cancer Research

Pankaj Agarwal, Kouros Owzar
2014 Cancer Informatics  
A proof-of-concept Hadoop cluster, set up for performance benchmarking of NGS read alignment, is described as an example of how to work with Hadoop.  ...  A broad overview of scalable computing is provided to set the context for a detailed description of Hadoop, a technology that is being rapidly adopted for large-scale distributed computing.  ...  Acknowledgment The authors thank the reviewers for insightful and helpful comments.  ... 
doi:10.4137/cin.s16344 pmid:25983539 pmcid:PMC4412427 fatcat:wpjhyuakejhirekbzouxtjdqnu
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