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Pablo A. Goloboff, P. A., De Laet, J. Ríos-Tamayo, D., Szumik, C. A. 2021. A reconsideration of inapplicable characters, and an approximation with step-matrix recoding. Cladistics, 37: 596-629.
De Laet, J. 2020b.
Anagallis, a program for parsimony analysis of character hierarchies. Version 1.03, 8 September 2020. Program and documentation.
[not peer reviewed]
Pdf of a dump of the built-in documentation of anagallis version 1.03,
including a discussion of the theory behind the program, of the high level structure of its main optimization algorithm, and of the scope and limits of that algorithm.
A gzipped tarfile that contains Linux and macOS executables and several files to get started with the program is available here.
Basic instructions, including how to get started once the gzipped tarfile is downloaded, can be found here.
De Laet, J. 2020a.
Anagallis, a program for parsimony analysis of character hierarchies. Version 1.02a, 27 May 2020. Program and documentation.
[not peer reviewed]
Pdf of a dump of the built-in documentation of anagallis version 1.02a.
De Laet, J. 2018a.
Anagallis, a program for parsimony analysis of character hierarchies. Version 1.01, 11 December 2018. Program and documentation.
[not peer reviewed]
Pdf of a dump of the built-in documentation of anagallis version 1.01.
This is the first version to include a high level description of the main optimization algorithm and a discussion of the scope and limits of that algorithm.
It is also the first version to include a macOS executable in addition to the Linux executable.
DOI 10.13140/RG.2.2.25157.29924.
De Laet, J. 2018b.
Anagallis, a program for parsimony analysis of character hierarchies. Version 0.998, 16 April 2018. Program and documentation.
[not peer reviewed]
Pdf of a dump of the built-in documentation of anagallis version 0.998, the first public beta version of the program.
DOI 10.13140/RG.2.2.35111.24487.
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. 7 pp. DOI 10.13140/RG.2.2.31309.54245. [not peer reviewed]
De Laet, J., Castroviejo-Fisher, S. 2015. Parsimony analysis of unaligned sequence data: an exchange. Pdf version of an ongoing exchange in ResearchGate. 16 pp. [not peer reviewed]
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.
De Laet, J. 2010. Letter to the editor. A problem in POY tree searches (and its work-around) when some sequences are observed to be absent in some terminals. Cladistics 26: 453-455.
Lindqvist, C., De Laet, J., Haynes, R.R., Aagesen, L., Keener, B. R., and Albert, V.A. 2006. Molecular phylogenetics of an aquatic plant lineage, Potamogetonaceae. Cladistics 22: 568-588.
De Laet, J. 2005a. Parsimony and the problem of inapplicables in sequence data. Pp. 81-116 in Albert, V.A. (ed.) Parsimony, phylogeny and genomics. Oxford University Press, ISBN 0-19-856493-7.
De Laet, J. 2005b. Pseudocode for some tree search algorithms in phylogenetics. Version 1.0. Manuscript distributed under the terms of the GNU Free Documentation License. 31 pp. [not peer reviewed]
Wheeler, W., Janies, D., and De Laet, J. 2004. Parallel computer processing in systematics. Pp. 247-250 in McGraw-Hill yearbook of science and technology. McGraw-Hill, ISBN 0-07-142784-8.
De Laet, J., and Wheeler, W. 2003. POY version 3.0.11. (Wheeler, Gladstein, and De Laet, May 6 2003). Command line documentation. 67 pp. [not peer reviewed]
Mészáros, S., De Laet, J., Goethals, V., Smets, E., and Nilsson, S. 2002. Cladistics of Gentianaceae: a morphological approach. Pp. 310-376 in: Struwe, L. and Albert V. A. (eds.) Gentianaceae: systematics and natural history. Cambridge University Press, ISBN 0-521-80999-1.
Vander Stappen, J., De Laet, J., Gama-López, S., Van Campenhout, S., and Volckaert, G. 2002 Phylogenetic analysis of Stylosanthes (Fabaceae) based on the internal transcribed spacer region (ITS) of nuclear ribosomal DNA. Plant Systematics and Evolution 234: 27-51.
Farris, J.S., Källersjö, M., and J. De Laet. 2001. Branch lengths do not indicate support – even in maximum likelihood. Cladistics 17: 298-299.
Farris, J.S., Kluge, A. G., and J. De Laet. 2001. Taxic revisions. Cladistics 17: 79-103.
De Laet, J. and Smets, E. 1999. Data decisiveness, missing entries, and the DD index. Cladistics 15: 25-37.
De Laet, J. and Smets, E. 1998a. On the TTSC-FTSC formulation of standard parsimony. Cladistics 14: 239-248.
De Laet, J., and Smets, E. 1998b. On the three-taxon approach to parsimony analysis. Cladistics 14: 363-381.
Ronse Decraene, L.P., De Laet, J., and Smets, E. 1998. Floral development and anatomy of Moringa oleifera (Moringaceae): what is the evidence for a capparalean or sapindalean affinity? Annals of Botany 82: 273-284.
De Laet, J. 1997. A reconsideration of three-item analysis, the use of implied weights in cladistics, and a practical application in Gentianaceae. Dissertation.
De Laet, J. and Smets, E. 1996. A commentary on the circumscription and evolution of the order Gentianales, with special emphasis on the position of the Rubiaceae. Pp. 11-18 in Robbrecht, E., Puff, C., and Smets, E. (eds.) Opera Botanica Belgica 7. Proceedings of the Second International Rubiaceae Conference. Meise, National Botanic Garden of Belgium, 13-15 September 1995. 432 p.
Ronse Decraene, L.P., De Laet, J., and Smets, E. 1996. Morphological studies in Zygophyllaceae II. The floral development and vascular anatomy of Peganum harmala. American Journal of Botany 83: 201-215.
Mészáros, S., De Laet, J., and Smets, E. 1996. Phylogeny of temperate Gentianaceae: a morphological approach. Systematic Botany 21: 153-168.
De Laet, J, Clinckemaillie, D., Jansen, S., and Smets, E. 1995. Floral ontogeny in the Plumbaginaceae. Journal of Plant Research 108: 289-304.
De Laet, J. 1995. Book review. Phyllotaxis: a systemic study in plant morphogenesis. Jean, R. V. Cambridge University Press, Cambridge, 1994, XIV + 386 p., ISBN/ISSN: 0-521-40482-7. Het Ingenieursblad. 52-53. [not peer reviewed]
De Laet, J. and Smets, E. 1994. Inleiding tot het cladisme. Belgian Journal of Botany 127: 207-229.
De Laet, J. 1989. Enkele beschouwingen rond de veredeling van de Amerikaanse Eik (Quercus rubra). De Boskrant 19: 10-17. [popular, not peer reviewed]