PAUP* Phylogenetic analysis using parsimony (*and other methods) Version 4

By Michael P. Cummings. 2000

8,956 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/90ebba3ccdcd60982aa54b5ff201c0ed63c5cb32

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Citations in the corpus

The phylogeny of the genus Nannochloropsis (Monodopsidaceae, Eustigmatophyceae), with descriptions of N. australis sp. nov. and Microchloropsis gen. nov. (2015, methodology): “MP analyses were performed with PAUP* 2.0b (Swofford 2002) and maximum likelihood (ML) analyses used the Garli 0.96 software (Zwickl 2006).”
Phylogeographic patterning in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes) reveals the signature of historical climatic oscillations (2006, methodology): “Phylogenetic data analyses were executed in paup*4 version beta 10 (Swofford, 2002) using parsimony (MP) and minimum evolution (ME) optimality criteria, as well as maximum likelihood (ML).”
A Phylogenetic Study of the Order Asterales Using One Morphological and Three Molecular Data Sets (2003, methodology): “The parsimony analysis was done with PAUP* 4.0b10 (Swofford 2001), using heuristic searches with random addition sequences (with 100 addition sequence replicates; when the morphological data set was analyzed separately, 1000 ad-”
Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade (2006, background): “A similar false pairing of paralogs could also result from extinct lineages and/or gene extinction (Figure 2, E and F).”
Phylogeny of Cyperaceae based on DNA sequence data - a new rbcL analysis (2007, positive): “Studies within subfamilies have focused on Caricoideae (Starr et al. 1999, 2003, 2004, in press; Yen and Olmstead 2000; VOLUME 23 73Cyperaceae Phylogeny Roalson et al. 2001), Cyperoideae (Muasya et al. 2000b, 2001, 2002; Zhang et al. 2004a, b) and Mapanioideae (Simpson et al. 2003).”
Rapid evolution and specialization following host colonization in a yucca moth (2000, methodology): “To evaluate sequence evolution between haplotypes, pairwise genetic distance estimates, and a neighbour-joining analysis were conducted for all unique haplotypes using PAUP* (Swofford, 1998).”
Mitochondrial differentiation and biogeography of Hyla meridionalis (Anura: Hylidae): an unusual phylogeographical pattern (2007, methodology): “Genetic divergence in pairwise comparisons was calculated using the software paup*4.0b10 (Swofford, 2002).”
Detecting and overcoming systematic errors in genome-scale phylogenies. (2007, methodology): “MP analyses were performed using PAUP* (Swofford, 2000), with tree bisection and reconnection search and 10 random additions of species.”
Associating larvae and adults of Chinese Hydropsychidae caddisflies (Insecta:Trichoptera) using DNA sequences (2007, methodology): “Phylograms were constructed independently from D2 and COI sequences using distance and neighborjoining in PAUP*4.0b10 (Swofford 2003).”
What is Geosaurus? Redescription of Geosaurus giganteus (Thalattosuchia: Metriorhynchidae) from the Upper Jurassic of Bayern, Germany (2009, methodology): “The cladistic analysis was carried out with PAUP 4.0b10 (Swofford, 2003), using a heuristic search algorithm with tree bisection reconnection (TBR) branch swapping (200 replicates).”