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Maximum parsimony (MP) analyses of the ITS and the combined chloroplast makers were carried out using PAUP* [ 51].
This strain can be classified as the alternative Type 1 subspecies based on phylogenetic analyses of the ITS region and MTLα idiomorphs (supplementary figs. S2 and S3, Supplementary Material online).
Maximum likelihood (ML) analyses of the ITS and ETS datasets were conducted separately using PhyML v. 3.1 (Guindon et al. 2010) following the strategy described in Mavrodiev et al. (2014) using sequence data from Mavrodiev et al. (2008 b, 2012).
So far in Italy, only three human cases have been identified by molecular methods; in these cases, this was enabled by the removal of Anisakis larvae from the stomach by endoscopy followed by PCR-RFLP analyses of the ITS of rDNA or sequences analysis of the mtDNA cox2 gene [ 10, 16, 17].
Separate parsimony analyses of the ITS (175 taxa, 799 nucleotides) and plastid (231 taxa, 5933 nucleotides) datasets were undertaken with the parsimony ratchet implemented in PAUPRat [ 26], to check for strongly supported phylogenetic conflicts (bootstrap percentages >75), before proceeding with analyses based on a total evidence approach using all characters.
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Fig. 1 The best ML tree from the analyses of the combined ITS and chloroplast trnL-F regions.
Wolfe et al. (2006) conducted the largest molecular phylogenetic study on Penstemon to date with 163 species included in their parsimony analyses of the nuclear ITS and chloroplast trnC-D and trnT-L regions.
The two halves of this exhibition, at the Hoover and the Cantor, offer visitors an opportunity to experience the Revolution in ways impossible through books and other after-the-fact analyses of the event and its aftermath.
In so holding, the Supreme Court noted that following the previous approach will "exclude from discretionary punishment many of the most culpable offenders, including the 'wanton and malicious pirate' who intentionally infringes a patent". Id. at 9. Various blogs have provided thorough analyses of the case and its implications.
In this paper we have undertaken further detailed analyses of the data in its continuous form.
Two comparative whole genome nucleotide sequence analyses of the evolved PB12, its parental JM101, and the wild type K-12 MG1655 strains were performed.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com