Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Sep;63(5):812-8.
doi: 10.1093/sysbio/syu031. Epub 2014 Apr 30.

A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0

Adam L Bazinet  1 , Derrick J Zwickl  2 , Michael P Cummings  2
Affiliations

A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0

Adam L Bazinet et al. Syst Biol. 2014 Sep.

Abstract

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.

PubMed Disclaimer

Figures

F<sc>igure</sc> 1.
Figure 1.
Properties of trees from multiple search replicates for a representative analysis using garli. a) The distribution of likelihood scores. b) The distribution of symmetric tree distances (as a fraction of the maximum possible value for the data set). Both measures are given as frequency and proportion.
F<sc>igure</sc> 2.
Figure 2.
Confidence intervals associated with the bootstrap probabilities observed in the majority rule consensus tree computed from 500 garli bootstrap replicates. Confidence intervals are given for three probabilities (0.90, 0.95, and 0.99).
F<sc>igure</sc> 3.
Figure 3.
Relationship between the number of search replicates (out of 100) returning the same topology as that of the best tree found and the estimated number of search replicates necessary to guarantee a particular probability of recovering that topology. Estimates are given at three probabilities (0.90, 0.95, 0.99).
F<sc>igure</sc> 4.
Figure 4.
Completion times of 719 analyses submitted to the garli web service for a recent six month period (2013-07-23 to 2014-01-23). Despite great variation in analysis parameters (e.g., data matrix size, substitution model used, number of replicates requested), ≈97% of analyses were completed in less than 24 hours.
See this image and copyright information in PMC

References

    1. Anderson D.P. Proceedings of the 5th IEEE/ACM International Workshop on Grid Computing GRID '04 IEEE Computer Society. Washington, DC, USA: 2004. BOINC: A system for public-resource computing and storage; pp. 4–10.
    1. Bazinet A.L. The Lattice Project: A Multi-model Grid Computing System. College Park: University of Maryland; 2009. Master's thesis.
    1. Bazinet A.L., Cummings M P. 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and PhD Forum. 2011. Computing the tree of life: Leveraging the power of desktop and service grids; pp. 1896–1902.
    1. Bazinet A.L., Cummings M.P., Mitter K.T., Mitter C.W. Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study. PLoS ONE. 2013;8:e82615. - PMC - PubMed
    1. Cummings M., Huskamp J. Grid computing. EDUCAUSE Review. 2005;40:116–117.

Publication types