7 References
Agnarsson, I., & Miller, J. A. (2008). Is AccTran better than DelTran? Cladistics, 24(6), 1032–1038. doi:10.1111/j.1096-0031.2008.00229.x
Brazeau, M. D., Guillerme, T., & Smith, M. R. (2017). Morphological phylogenetic analysis with inapplicable data. bioR\(\chi\)iv. doi:10.1101/209775
De Laet, J. (2005). Parsimony and the problem of inapplicables in sequence data. In V. Albert (Ed.), Parsimony, phylogeny and genomics (pp. 81–116). Oxford University Press.
De Laet, J. (2015). Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not minimization of operationally defined total cost or minimization of equally weighted transformations. Cladistics, 31, 550–567. doi:10.1111/cla.12098
De Laet, J. (2017). A note on Brazeau et al.’s (2017) algorithm for characters with inapplicable data, illustrated with an analysis of their Fig. 3d using anagallis, a program for parsimony analysis of character hierarchies. doi:10.13140/RG.2.2.31309.54245
Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Biology, 20(4), 406–416. doi:10.1093/sysbio/20.4.406
Goloboff, P. A., & Catalano, S. A. (2016). TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics, 32(3), 221–238. doi:10.1111/cla.12160
Maddison, W. P. (1993). Missing data versus missing characters in phylogenetic analysis. Systematic Biology, 42(4), 576–581. doi:10.1093/sysbio/42.4.576
Ronquist, F., Teslenko, M., Mark, P. van der, Ayres, D. L., Darling, A., Hohna, S., … Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61(3), 539–42.
Sereno, P. C. (2007). Logical basis for morphological characters in phylogenetics. Cladistics, 23(6), 565–587. doi:10.1111/j.1096-0031.2007.00161.x
Stamatakis, A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9), 1312–1313. doi:10.1093/bioinformatics/btu033
Swofford, D. L. (2001). PAUP*: Phylogenetic analysis using parsimony (and other methods) 4.0. B5.