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

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. [garli, gateway, grid computing, maximum likelihood, molecular evolution portal, phylogenetics, web service.]

[1]  Ian Foster,et al.  The Grid 2 - Blueprint for a New Computing Infrastructure, Second Edition , 1998, The Grid 2, 2nd Edition.

[2]  Sonia Sharama,et al.  Grid Computing , 2004, Lecture Notes in Computer Science.

[3]  M. P. Cummings,et al.  A Molecular Phylogeny for Yponomeutoidea (Insecta, Lepidoptera, Ditrysia) and Its Implications for Classification, Biogeography and the Evolution of Host Plant Use , 2013, PloS one.

[4]  Miron Livny,et al.  Condor-a hunter of idle workstations , 1988, [1988] Proceedings. The 8th International Conference on Distributed.

[5]  Mark A. Miller,et al.  Creating the CIPRES Science Gateway for inference of large phylogenetic trees , 2010, 2010 Gateway Computing Environments Workshop (GCE).

[6]  David P. Anderson,et al.  BOINC: a system for public-resource computing and storage , 2004, Fifth IEEE/ACM International Workshop on Grid Computing.

[7]  M. P. Cummings,et al.  Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae) , 2011, BMC Evolutionary Biology.

[8]  Daniel S. Myers,et al.  Necessity is the mother of invention: a simple grid computing system using commodity tools , 2003, J. Parallel Distributed Comput..

[9]  Paul O. Lewis,et al.  NCL: a C++ class library for interpreting data files in NEXUS format , 2003, Bioinform..

[10]  Cynthia Parr,et al.  A Large-Scale, Higher-Level, Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies) , 2013, PloS one.

[11]  Surendra Kumar,et al.  AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses , 2009, BMC Bioinformatics.

[12]  Derrick J. Zwickl Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion , 2006 .

[13]  Rubén Sánchez,et al.  Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing , 2011, Nucleic Acids Res..

[14]  M. P. Cummings,et al.  Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study , 2013, PloS one.

[15]  Alexandros Stamatakis,et al.  How Many Bootstrap Replicates Are Necessary? , 2009, RECOMB.

[16]  S. Hedges The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies. , 1992, Molecular biology and evolution.

[17]  Alexandros Stamatakis,et al.  How Many Bootstrap Replicates Are Necessary? , 2009, RECOMB.

[18]  D. Robinson,et al.  Comparison of phylogenetic trees , 1981 .

[19]  Adam L. Bazinet The Lattice Project: A multi-model grid computing system , 2009 .

[20]  Pierre Tufféry,et al.  BIOINFORMATICS ORIGINAL PAPER , 2022 .

[21]  Jeet Sukumaran,et al.  DendroPy: a Python library for phylogenetic computing , 2010, Bioinform..

[22]  Barath Raghavan,et al.  The energy and emergy of the internet , 2011, HotNets-X.

[23]  Michael P. Cummings,et al.  Computing the Tree of Life: Leveraging the Power of Desktop and Service Grids , 2011, 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum.

[24]  D. Janzen,et al.  Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study , 2009, BMC Evolutionary Biology.