PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)]

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SYSTEMATICS OF GRATELOUPIA FILICINA (HALYMENIACEAE, RHODOPHYTA), BASED ON rbcL SEQUENCE ANALYSES AND MORPHOLOGICAL EVIDENCE, INCLUDING THE REINSTATEMENT OF G. MINIMA AND THE DESCRIPTION OF G. CAPENSIS SP. NOV. 1 (2005, methodology): “…data at the 50 and 30 ends of the rbcL sequences, the first 107 and last 102 sites of 1467-bp gene were excluded from the analyses, leaving a total of 1259 bp. Maximum parsimony (MP), neighbor joining (NJ), and maximum likelihood (ML) analyses were performed using PAUP 4.0b10 (Swofford 2002).”
SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation (2014, methodology): “Computer programs such as MUSCLE [4], CLUSTALW [5], MAFFT [6] or BLAST [7] could be used to make either multiple individual pairwise sequence alignments or a single multiple sequence alignment and other programs such as MEGA5 [8], PHYLIP [9], PAUP [10] or GENEIOUS (http://www.”
A general suite of fungal endophytes dominate the roots of two dominant grasses in a semiarid grassland (2010, methodology): “A phylogenetic tree that only included representative sequences of the OTUs obtained with the program DOTUR at 99% similarity was constructed using parsimony analysis with PAUP 4.0b10 (Swofford, 2002).”
Botryosphaeriaceae associated with Terminalia catappa in Cameroon, South Africa and Madagascar (2010, methodology): “0b10 (Swofford 2001) where a final manual alignment was made.”