If using the rooted SPR distance, cite Whidden et al. (2013); for the unrooted SPR distance, it's Whidden and Matsen (2019). A citation to the R package (Smith 2019) would also be welcome.

Whidden C, Beiko R, Zeh N (2013). “Fixed-Parameter Algorithms for Maximum Agreement Forests.” SIAM Journal on Computing, 42, 1431-–1466. doi:10.1137/110845045.

Whidden C, Matsen FA (2019). “Calculating the Unrooted Subtree-Prune-and-Regraft Distance.” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16, 898–911. doi:10.1109/TCBB.2018.2802911.

Whidden C, Zeh N, Beiko R (2014). “Supertrees based on the subtree prune-and-regraft distance.” Systematic Biology, 63, 566–581. doi:10.1093/sysbio/syu023.

Smith MR (2019). TBRDist: Rearrangement Distances Between Phylogenetic Trees. doi:10.5281/zenodo.3548333, R package version 2.0.0.

Corresponding BibTeX entries:

  @Article{Whidden2013,
    title = {Fixed-Parameter Algorithms for Maximum Agreement Forests},
    author = {Chris Whidden and RG Beiko and N Zeh},
    year = {2013},
    journal = {SIAM Journal on Computing},
    volume = {42},
    pages = {1431-–1466},
    doi = {10.1137/110845045},
  }

  @Article{Whidden2019,
    title = {Calculating the Unrooted Subtree-Prune-and-Regraft
      Distance.},
    author = {Chris Whidden and Frederick A. Matsen},
    journal = {IEEE/ACM Transactions on Computational Biology and
      Bioinformatics},
    issue = {3},
    volume = {16},
    pages = {898--911},
    year = {2019},
    doi = {10.1109/TCBB.2018.2802911},
  }

  @Article{Whidden2014,
    title = {Supertrees based on the subtree prune-and-regraft
      distance},
    author = {Chris Whidden and N Zeh and RG Beiko},
    year = {2014},
    journal = {Systematic Biology},
    volume = {63},
    pages = {566--581},
    doi = {10.1093/sysbio/syu023},
  }

  @Manual{Smith2019,
    title = {TBRDist: Rearrangement Distances Between Phylogenetic
      Trees},
    author = {Martin R. Smith},
    note = {R package version 2.0.0},
    publisher = {Comprehensive R Archive Network},
    year = {2019},
    doi = {10.5281/zenodo.3548333},
  }