Skip to content

Citation

If you use the software in a publication, please cite the software, the papers describing the method, and the appropriate citation for the external tools.

Algorithm citations

  • Liu, K., Raghavan, S., Nelesen, S., Linder, C. R., & Warnow, T. (2009). Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science, 324(5934), 1561–1564. https://doi.org/10.1126/science.1171243
  • Liu, K., Warnow, T. J., Holder, M. T., Nelesen, S., Yu, J., Stamatakis, A., & Linder, C. R. (2012). SATé-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Systematic Biology, 61(1), 90–106. https://doi.org/10.1093/sysbio/syr095

Citations for the SATé software itself and its dependencies

  • Jiaye Yu, and Mark T. Holder "SATé version VERSION_NUMBER_HERE" from http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED." (for version 1.2 or earlier)
  • Jiaye Yu, Mark T. Holder, Jeet Sukumaran, and Siavash Mirarab "SATé version VERSION_NUMBER_HERE" from http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED." (for version 1.2.1 to 2.1.0)
  • Jiaye Yu, Mark T. Holder, Jeet Sukumaran, Siavash Mirarab, and Jamie Oaks "SATé version VERSION_NUMBER_HERE" from http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED." (for version 2.2.0 or later)
  • Sukumaran, J. and Mark T. Holder. 2010. "DendroPy: A Python library for phylogenetic computing". Bioinformatics 26: 1569-1571. (for all SATé versions from this website)

External tool citations

Please remember to cite the aligner and tree inference tools that you use during the course of a SATé run. The exact citation will depend on what tools you choose to use: