TreeSwift: A massively scalable Python']Python tree package

被引：15
|
作者：
Moshiri, N. [1 ]
机构：
[1] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA
来源：
SOFTWAREX | 2020年 / 11卷
关键词：
Phylogenetics; Tree traversal; Scalable; !text type='Python']Python[!/text;
D O I：
10.1016/j.softx.2020.100436
中图分类号：
TP31 [计算机软件];
学科分类号：
081202 ; 0835 ;
摘要：
Phylogenetic trees are essential to evolutionary biology, and numerous methods exist that attempt to extract phylogenetic information applicable to a wide range of disciplines, such as epidemiology and metagenomics. Currently, the three main Python packages for trees are Bio.Phylo, DendroPy, and the ETE Toolkit, but as dataset sizes grow, parsing and manipulating ultra-large trees becomes impractical for these tools. To address this issue, we present TreeSwift, a user-friendly and massively scalable Python package for traversing and manipulating trees that is ideal for algorithms performed on ultra-large trees. (C) 2020 The Author. Published by Elsevier B.V.
引用
收藏
页数：4
相关论文
共 50 条
  • [21] CosmoFlow: Python']Python package for cosmological correlators
    Werth, Denis
    Pinol, Lucas
    Renaux-Petel, Sebastien
    CLASSICAL AND QUANTUM GRAVITY, 2024, 41 (17)
  • [22] WavePy: A Python']Python Package for Wave Optics
    Beck, Jeffrey
    Bekins, Celina
    Bos, Jeremy P.
    LONG-RANGE IMAGING, 2016, 9846
  • [23] matplotlib - A portable python']python plotting package
    Barrett, P
    Hunter, J
    Miller, JT
    Hsu, JC
    Greenfield, P
    Astronomical Data Analysis Software and Systems XIV, Proceedings, 2005, 347 : 91 - 95
  • [24] TDCRPy: A python']python package for TDCR measurements
    Coulon, Romain
    Hu, Jialin
    APPLIED RADIATION AND ISOTOPES, 2024, 214
  • [25] The Multitaper Spectrum Analysis Package in Python']Python
    Prieto, German A.
    SEISMOLOGICAL RESEARCH LETTERS, 2022, 93 (03) : 1922 - 1929
  • [26] Megaman: Scalable Manifold Learning in Python']Python
    McQueen, James
    Meila, Marina
    VanderPlas, Jacob
    Zhang, Zhongyue
    JOURNAL OF MACHINE LEARNING RESEARCH, 2016, 17
  • [27] Scalable Parallel Programming in Python']Python with Parsl
    Babuji, Yadu
    Woodard, Anna
    Li, Zhuozhao
    Katz, Daniel S.
    Clifford, Ben
    Foster, Ian
    Wilde, Michael
    Chard, Kyle
    PEARC '19: PROCEEDINGS OF THE PRACTICE AND EXPERIENCE IN ADVANCED RESEARCH COMPUTING ON RISE OF THE MACHINES (LEARNING), 2019,
  • [28] scFates: a scalable python']python package for advanced pseudotime and bifurcation analysis from single-cell data
    Faure, Louis
    Soldatov, Ruslan
    Kharchenko, Peter, V
    Adameyko, Igor
    BIOINFORMATICS, 2023, 39 (01)
  • [29] Scedar: A scalable Python']Python package for single-cell RNA-seq exploratory data analysis
    Zhang, Yuanchao
    Kim, Man S.
    Reichenberger, Erin R.
    Stear, Ben
    Taylor, Deanne M.
    PLOS COMPUTATIONAL BIOLOGY, 2020, 16 (04)
  • [30] TextCL: A Python']Python package for NLP preprocessing tasks
    Petukhova, Alina
    Fachada, Nuno
    SOFTWAREX, 2022, 19
12345