PAUP* 4.0 : Phylogenetic Analysis Using Parsimony

By David L. Swofford. 2002

1,094 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/8d4a902c43eac6fd9641261d3b62b631fb16a7b0

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Citations in the corpus

• Falling apart and merging: diversification of slender salamanders (Plethodontidae: Batrachoseps) in the American West (2002, methodology): “Base composition, stationarity of base composition, pairwise divergences and number of variable and informative sites were calculated in PAUP*4.0b6(Altivec) (Swofford, 2001).”
• DNA barcoding the floras of biodiversity hotspots (2008, methodology): “Pairwise distances were calculated with PAUP4b10 (38) and the best-fitting model as given by applying MODELTEST 3.”
• Calonectria species and their Cylindrocladium anamorphs: species with sphaeropedunculate vesicles (2004, methodology): “The phylogenetic analyses of sequence data were done using PAUP (Phylogenetic Analysis Using Parsimony) v. 4.0b10 (Swofford 2000).”
• Eyespot of Cereals Revisited: ITS phylogeny Reveals New Species Relationships (2003, methodology): “0b10 (Swofford, 2000).”
• Cylindrocarpon species associated with apple tree roots in South Africa and their quantification using real-time PCR (2011, methodology): “Maximum parsimony and distance analysis were conducted in PAUP (Phylogenetic Analysis Using Parsimony) 4.0b10 (Swofford 2002).”
• First Recorded Parasitoid from China of Agrilus planipennis: A New Species of Spathius (Hymenoptera: Braconidae: Doryctinae) (2005, methodology): “Data were analyzed in two ways: 1) maximum parsimony by using PAUP* 4.0 (Swofford 2001), by using a branch-and-bound search and 2) Bayesian analysis by using MrBayes3 (Ronquist and Huelsenbeck 2003), with models selected by MrModeltest 2.0 (Nylander 2002)ÑF81 for 16S, HKY for 28S, GTR G for COIÑ…”
• Phylogeny and evolution of the green lizards, Lacerta spp. (Squamata: Lacertidae) based on mitochondrial and nuclear DNA sequences (2005, methodology): “They were then imported into PAUP∗ 4.0b10 (Swofford, 2003) for phylogenetic analyses.”
• Lignicolous freshwater fungi from China II: Novel Distoseptispora (Distoseptisporaceae) species from northwestern Yunnan Province and a suggested unified method for studying lignicolous freshwater fungi (2018, methodology): “Phylogenetic analyses were performed by using PAUP v.4.0b10 (Swofford 2002) for maximum parsimony (MP) and MrBayes v.3.2.2 (Ronquist et al. 2012) for Bayesian analyses.”
• Phylogenetic analysis of ascomycete yeasts that form coenzyme Q-9 and the proposal of the new genera Babjeviella, Meyerozyma, Millerozyma, Priceomyces, and Scheffersomyces (2010, unknown): “063a (Swofford 1998).”
• Phylogenetic reassessment of Mycosphaerella spp. and their anamorphs occurring on Eucalyptus (2004, unknown): “Phylogenetic analyses of sequence data were done using PAUP (Phylogenetic Analysis Using Parsimony) v. 4.0b10 (Swofford 2000).”
• Applying the Bootstrap in Phylogeny Reconstruction (2003, methodology): “Fast search options (e.g., bootstrapping under parsimony without branch swapping, in PAUP* 4.0, Swofford, 1998; parsimony jackknifing, Farris et al., 1996; see below), coupled with correctional methods, may provide support levels that are less affected by increasing numbers of taxa.”
• New universal matK primers for DNA barcoding angiosperms (2011, methodology): “Ten 600-bp data subsets were generated by sampling the data set of the entire length and analyzed with PAUP 4.0b10 (Swofford, 2000) to reconstruct the phylogeny.”
• A comparison of two DNA barcode markers for species discrimination in the red algal family Kallymeniaceae (Gigartinales, Florideophyceae), with a description of Euthora timburtonii sp. nov. (2010, methodology): “Published by NRC Research Press were conducted in PAUP* 4.0b10 (Swofford 2002).”