PAUP: Phylogenetic analysis using parsimony (and other methods), Version 4.0b10

By D. Swofford. 2002

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Biogeography of the Mesoamerican Cichlidae (Teleostei: Heroini): colonization through the GAARlandia land bridge and early diversification (2013, methodology): “An optimal model of evolution for each data partition according to Akaike’s information criterion was selected using MrModelTest 2.2 (Nylander, 2004) and paup* 4.0b10 (Swofford, 2003).”
Phylogeny of Vitaceae based on the nuclear GAI1 gene sequences (2007, methodology): “Parsimony analyses were conducted using PAUP* version 4.0b10 (Swofford 2003) with heuristic search, random taxon addition, 100 random-addition replicates, tree-bisectionreconnection (TBR) branch swapping, and the Mulpars and Steepest descent options.”
EARLY EVOLUTIONARY HISTORY OF DINOFLAGELLATES AND APICOMPLEXANS (ALVEOLATA) AS INFERRED FROM HSP90 AND ACTIN PHYLOGENIES 1 (2004, methodology): “A heuristic search was performed using PAUP* 4.0 (Swofford 1999) with ACCTRAN character state optimization, tree bisection reconnection branch swapping, random step-wise addition of taxa (10 input order jumbles), and MULTREES on.”