This software benefited from funding provided to Jamie Oaks from the National Science Foundation (DBI 1308885 and DEB 1656004).
Ecoevolity comes bundled with the Nexus Class Library Version 2.1.18 (Copyright Paul O. Lewis and Mark T. Holder; licensed under a BSD License). NCL is used for parsing the nexus input files.
Ecoevolity also comes bundled with yaml-cpp commit 7d2873c (master branch) (Copyright Jesse Beder; licensed under a BSD-like License). Yaml-cpp is used for parsing ecoevolity configuration files.
Ecoevolity also comes bundled with cpp-optparse (Copyright Johannes Weiß; MIT License). Cpp-optparse is used to parse command-line options.
The likelihood machinery in ecoevolity was adapted from the java code in SNAPP which is a package for BEAST 2 (GNU Lesser General Public License Version 2.1). Citation: Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., and Roychoudhury, A. 2012. Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution, 29(8): 1917–1932. https://doi.org/10.1093/molbev/mss086
Some of the convenience functions for calculating properties of Dirichlet
processes were inspired by functions within
util.h from the software
package DPPDiv Version
1.0b (Copyright Tracy Heath, Mark Holder, and John Huelsenback; licensed under
GPL v3; http://phylo.bio.ku.edu/content/tracy-heath-dppdiv).