dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units

被引：11
|
作者：
Gutenkunst, Ryan N. [1 ]
机构：
[1] Univ Arizona, Dept Mol & Cellular Biol, Tucson, AZ 85721 USA
来源：
MOLECULAR BIOLOGY AND EVOLUTION | 2021年 / 38卷 / 05期
基金：
美国国家卫生研究院;
关键词：
population genetics; demographic history; GPU computing; dadi; DEMOGRAPHIC HISTORY;
D O I：
10.1093/molbev/msaa305
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
dadi is a popular but computationally intensive program for inferring models of demographic history and natural selection from population genetic data. I show that running dadi on a Graphics Processing Unit can dramatically speed computation compared with the CPU implementation, with minimal user burden. Motivated by this speed increase, I also extended dadi to four- and five-population models.
引用
收藏
页码：2177 / 2178
页数：2
相关论文
共 50 条
  • [1] Accelerating parameter inference with graphics processing units
    Wysocki, D.
    O'Shaughnessy, R.
    Lange, Jacob
    Fang, Yao-Lung L.
    PHYSICAL REVIEW D, 2019, 99 (08)
  • [2] Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA
    Liu, Weiguo
    Schmidt, Bertil
    Voss, Gerrit
    Mueller-Wittig, Wolfgang
    COMPUTER PHYSICS COMMUNICATIONS, 2008, 179 (09) : 634 - 641
  • [3] Accelerating FCM neural network classifier using graphics processing units with CUDA
    Wang, Lin
    Yang, Bo
    Chen, Yuehui
    Chen, Zhenxiang
    Sun, Hongwei
    APPLIED INTELLIGENCE, 2014, 40 (01) : 143 - 153
  • [4] Accelerating FCM neural network classifier using graphics processing units with CUDA
    Lin Wang
    Bo Yang
    Yuehui Chen
    Zhenxiang Chen
    Hongwei Sun
    Applied Intelligence, 2014, 40 : 143 - 153
  • [5] Accelerating Parallel Magnetic Resonance Image Reconstruction on Graphics Processing Units Using CUDA
    Inam, Omair
    Qureshi, Mahmood
    Akram, Hamza
    Omer, Hammad
    Laraib, Zoia
    2019 IEEE 2ND INTERNATIONAL CONFERENCE ON INFORMATION AND COMPUTER TECHNOLOGIES (ICICT), 2019, : 109 - 113
  • [6] CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units
    Liu, Yongchao
    Schmidt, Bertil
    Liu, Weiguo
    Maskell, Douglas L.
    PATTERN RECOGNITION LETTERS, 2010, 31 (14) : 2170 - 2177
  • [7] Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units
    Jiang, Rui
    Zeng, Feng
    Zhang, Wangshu
    Wu, Xuebing
    Yu, Zhihong
    2009 INTERNATIONAL JOINT CONFERENCE ON BIOINFORMATICS, SYSTEMS BIOLOGY AND INTELLIGENT COMPUTING, PROCEEDINGS, 2009, : 70 - +
  • [8] Efficient magnetohydrodynamic simulations on graphics processing units with CUDA
    Wong, Hon-Cheng
    Wong, Un-Hong
    Feng, Xueshang
    Tang, Zesheng
    COMPUTER PHYSICS COMMUNICATIONS, 2011, 182 (10) : 2132 - 2160
  • [9] MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA
    Liu, Yongchao
    Schmidt, Bertil
    Maskell, Douglas L.
    2009 20TH IEEE INTERNATIONAL CONFERENCE ON APPLICATION-SPECIFIC SYSTEMS, ARCHITECTURES AND PROCESSORS, 2009, : 121 - 128
  • [10] Accelerating NTRU Encryption with Graphics Processing Units
    Bai, Tianyu
    Davis, Spencer
    Li, Juanjuan
    Gu, Ying
    Jiang, Hai
    INTERNATIONAL JOURNAL OF NETWORKED AND DISTRIBUTED COMPUTING, 2014, 2 (04) : 250 - 258
12345