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Citation Information

Citing KSU's HPC Facilities and Resources

The recommendation of the KSU Office of Research for acknowledging and citing KSU's HPC is as follows:

Recommended Citation:

"This work was supported in part by research computing resources and technical expertise via a partnership between Kennesaw State University's Office of the Vice President for Research and the Office of the CIO and Vice President for Information Technology [1]."

[1] Boyle, Tom and Aygun, Ramazan, "Kennesaw State University HPC Facilities and Resources" (2021). Digital Commons Training Materials. 10. https://digitalcommons.kennesaw.edu/training/10

Citing Individual Software Packages

Many software packages on the HPC have citation requirements in addition to the above recommendation. Where available, we've placed the citation information in the online help for each module. You can obtain this information by looking at the online software index about the module on this website or while logged into the HPC by using the module help command looking for a section labeled 'Citation Information':

[barney@hpc ~]$ module help PhyML
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Module Specific Help for /data/Apps/Modules/Software/PhyML/3.3.20200621:

        This module file will configure your environment for
        PhyML/3.3.20200621 on the Kennesaw State HPC Cluster.

        PhyML is a software package that uses modern statistical approaches
        to analyze alignments of nucleotide or amino acid sequences in a
        phylogenetic framework. The main tool in this package builds
        phylogenies under the maximum likelihood criterion. It implements
        many substitution models coupled to efficient options to search
        the space of phylogenetic tree topologies. PhyTime is another tool
        in the PhyML package that focuses on divergence date estimation
        in a Bayesian setting. The main strengths of PhyTime lies in its
        ability to accommodate for uncertainty in the placement of fossil
        calibration and the use of realistic models of rate variation along
        the tree. Finally, PhyREX fits the spatial-Lambda-Fleming-Viot model
        to geo-referenced genetic data. This model is similar to the
        structured coalescent but assumes that individuals are distributed
        along a spatial continuum rather than discrete demes. PhyREX can be
        used to estimate population densities and rates of dispersal. Its
        output can be processed by treeannotator (from the BEAST package) as
        well as SPREAD.

        Version:        3.3.20200621
        Official Site:  https://github.com/stephaneguindon/phyml
        Install Date:   10-Apr-2019

        TAGS:           Phylogeny, Maximum Likelihood

        *************************
        ** Citation Inforation **
        *************************

        If you use PhyML in your research, please cite:

          * New algorithms and methods to estimate maximum-likelihood
            phylogenies: assessing the performance of PhyML 3.0 S Guindon, JF
            Dufayard, V Lefort, M Anisimova, W Hordijk, O Gascuel Systematic
            Biology 59 (3), 307-321, 2010.

          * Accounting for calibration uncertainty: Bayesian molecular dating
            as a “doubly intractable” problem S Guindon Systematic Biology 67
            (4), 651–661, 2018.

          * Demographic inference under the coalescent in a spatial continuum
            S Guindon, H Guo, D Welch Theoretical Population Biology 111,
            43-50, 2016.

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