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Papers Referenced in TreeSearch Optimization Work

Tracking citations for write-up purposes.

Search Algorithm Infrastructure

Key	Citation	Relevance
Goloboff1999	Goloboff, P.A. (1999). Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15(4): 415–428. doi:10.1006/clad.1999.0122	Foundational: sectorial searches (XSS/RSS/CSS), drift search, outer-cycle interleaving pattern (§2.3)
Nixon1999	Nixon, K.C. (1999). The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15(4): 407–414. doi:10.1111/j.1096-0031.1999.tb00277.x	Parsimony ratchet: weight perturbation to escape local optima
Goloboff2016	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	TNT reference: xmult, driven search pipeline

Wagner Tree Construction

Key	Citation	Relevance
Goloboff2014	Goloboff, P.A. (2014). Extended implied weighting. Cladistics 30(3): 260–272. doi:10.1111/cla.12047	§3.3: biased taxon-addition order for Wagner trees; stochastic sampling from informativeness-weighted distribution (T-188)
Kluge1969	Kluge, A.G. & Farris, J.S. (1969). Quantitative phyletics and the evolution of anurans. Systematic Zoology 18(1): 1–32.	Original Wagner tree construction

NNI Perturbation

Key	Citation	Relevance
Nguyen2015	Nguyen, L.-T., Schmidt, H.A., von Haeseler, A. & Minh, B.Q. (2015). IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Molecular Biology and Evolution 32(1): 268–274. doi:10.1093/molbev/msu300	Stochastic NNI-perturbation strategy (doRandomNNIs); topology-space escape mechanism (T-186)

Parsimony Scoring

Key	Citation	Relevance
Fitch1971	Fitch, W.M. (1971). Toward defining the course of evolution: Minimum change for a specific tree topology. Systematic Zoology 20(4): 406–416.	Standard Fitch parsimony algorithm
Brazeau2019	Brazeau, M.D., Guillerme, T. & Smith, M.R. (2019). An algorithm for morphological phylogenetic analysis with inapplicable data. Systematic Biology 68(4): 619–631. doi:10.1093/sysbio/syy083	Three-pass inapplicable algorithm (NA scoring)

Inapplicable-Handling Alternatives

Key	Citation	Relevance
Hopkins2021	Hopkins, M.J. & St. John, K. (2021). A new approach to inapplicable characters in phylogenetics. Systematic Biology 70(4): 764–781.	HSJ dissimilarity-metric scoring (T-116–T-118)
Goloboff2021	Goloboff, P.A., Torres, A. & Arias, J.S. (2021). Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology. Cladistics 37(6): 569–588.	X-transformation recoding for step-matrix inapplicable handling (T-122)

Implied Weighting

Key	Citation	Relevance
Goloboff1993	Goloboff, P.A. (1993). Estimating character weights during tree search. Cladistics 9(1): 83–91.	Implied weighting: k/(e+k)
Goloboff2018	Goloboff, P.A., Torres, A. & Arias, J.S. (2018). Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology. Cladistics 35(4): 407–437. doi:10.1111/cla.12prior	Recommended k≈10; IW outperforms EW on morphological data

Resampling

Key	Citation	Relevance
Goloboff2003	Goloboff, P.A. et al. (2003). Improvements to resampling measures of group support. Cladistics 19(4): 324–332. doi:10.1016/S0748-3007(03)00060-4	Symmetric resampling (jackknife/bootstrap frequencies)

Profile Parsimony

Key	Citation	Relevance
Faith2001	Faith, D.P. & Trueman, J.W.H. (2001). Towards an inclusive philosophy for phylogenetic inference. Systematic Biology 50(3): 331–350. doi:10.1080/10635150118627	Profile parsimony: information-based character weights