A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0

被引：170
作者：
Bazinet, Adam L. [1 ]
Zwickl, Derrick J. [2 ]
Cummings, Michael P. [1 ]
机构：
[1] Univ Maryland, Ctr Bioinformat & Computat Biol, College Pk, MD 20742 USA
[2] Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA
来源：
SYSTEMATIC BIOLOGY | 2014年 / 63卷 / 05期
基金：
美国国家科学基金会;
关键词：
GARLI; gateway; grid computing; maximum likelihood; molecular evolution portal; phylogenetics; web service; EVOLUTION; LIBRARY; MOTHS;
D O I：
10.1093/sysbio/syu031
中图分类号：
Q [生物科学];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
We introduce molecularevolution. org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a GARLI 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The GARLI web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the GARLI web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results.
引用
收藏
页码：812 / 818
页数：7
相关论文
共 24 条
  • [1] BOINC: A system for public-resource computing and storage
    Anderson, DP
    [J]. FIFTH IEEE/ACM INTERNATIONAL WORKSHOP ON GRID COMPUTING, PROCEEDINGS, 2004, : 4 - 10
  • [2] [Anonymous], 2006, GENETIC ALGORITHM AP
  • [3] Bazinet A. L., 2011, 2011 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum, P1896, DOI 10.1109/IPDPS.2011.344
  • [4] Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study
    Bazinet, Adam L.
    Cummings, Michael P.
    Mitter, Kim T.
    Mitter, Charles W.
    [J]. PLOS ONE, 2013, 8 (12):
  • [5] BazinetA L., 2009, THESIS U MARYLAND CO
  • [6] Cummings M.P., 2005, Educause Review, V40, P116
  • [7] Foster I, 1999, GRID: BLUEPRINT FOR A NEW COMPUTING INFRASTRUCTURE, P259
  • [8] HEDGES SB, 1992, MOL BIOL EVOL, V9, P366
  • [9] Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae)
    Kawahara, Akito Y.
    Ohshima, Issei
    Kawakita, Atsushi
    Regier, Jerome C.
    Mitter, Charles
    Cummings, Michael P.
    Davis, Donald R.
    Wagner, David L.
    De Prins, Jurate
    Lopez-Vaamonde, Carlos
    [J]. BMC EVOLUTIONARY BIOLOGY, 2011, 11
  • [10] AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses
    Kumar, Surendra
    Skjaeveland, Asmund
    Orr, Russell J. S.
    Enger, Pal
    Ruden, Torgeir
    Mevik, Bjorn-Helge
    Burki, Fabien
    Botnen, Andreas
    Shalchian-Tabrizi, Kamran
    [J]. BMC BIOINFORMATICS, 2009, 10 : 357
123