Jonathan D. Marcot and David L. Fox

StrataPhy is a computer program designed to perform stratocladistic analysis. Stratocladistic analysis minimizes ad hoc hypotheses of both character homoplasy and non-preservation in the fossil record allowing for the simultaneous analysis of morphologic and stratigraphic data. Prior to StrataPhy, stratocladistic analyses required multiple computer programs and manual branch arrangement. StrataPhy employs full TBR branch swapping coupled with an integrated search for the optimal assignment of taxa as ancestors. The algorithms involved in a StrataPhy stratocladistic search are discussed in detail. StrataPhy reads standard NEXUS formatted files, and additional formatting required for a StrataPhy analysis is described. We also describe a reanalysis of a previously published data set that emphasizes the potential utility of StrataPhy over previous approaches to stratocladistic analysis.

Jonathan D. Marcot. Department of Geology and Geophysics, University of Minnesota, 310 Pillsbury Drive SE, Minneapolis, MN, 55455-0219
Current address: Department of Animal Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801 USA
David L. Fox. Department of Geology and Geophysics, University of Minnesota, 310 Pillsbury Drive SE, Minneapolis, MN, 55455-0219 USA

KEY WORDS: computer program, software, phylogenetic inference, phylogeny, stratocladistics

PE Article Number: 11.1.5A
Copyright: Paleontological Society March 2008
Submission: 24 September 2006. Acceptance: 4 February 2008