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The alignments and tree files generated in this study have been deposited in figshare (https://doi.org/10.6084/m9.figshare.12347216) (ref.30). Code availability The script of the Bowker’s test score-based site-exclusion method is available asSupplementary Software. ...
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The latter expands on earlier phylogenetic studies across Cyprinoidei, Cobitoidei, and Cypriniformes based on these same loci from the Cypriniformes Tree of Life project (e.g. Chen & Mayden 2009; Chen et al. 2009; Mayden & Chen 2010), and also explores the effect of gene choice on ...
(Additional file 2: Table S6). The concatenated data matrix encompassed 3,665 characters. The ML analysis conducted on the three genes resulted in an optimal single tree (-lnL = 37562.0677). In particular, a monophyletic group comprising six representativeB. bracteatasamples was identified (...
Notes for genera: Ascomycota 2017, Fungal Diversity Fungal diversity notes 367–490: taxonomic and phylogenetic contributions to fungal taxa 2016, Fungal Diversity Fungal diversity notes 253–366: taxonomic and phylogenetic contributions to fungal taxa 2016, Fungal Diversity View all citing articles on ...
https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/appnote_16s_sequencing.pdf. Accessed Oct 2017. Albanese D, De Filippo C, Cavalieri D, Donati C. Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting. PLoS Comput Biol. 2015; 11(3)...
We formulate an optimization problem, called the k-shrink problem, that seeks to find k leaves that could be removed to maximally reduce the tree diameter. We present an algorithm to find the exact solution for this problem in polynomial time. We then use several statistical tests to find ...
The maximum clade credibility tree was constructed on the basis of the best-fitting model combination, which was run for 50 million generations, sampling every 5,000 generations and treating the first 10% of the iterations as burn-in. The 109 Sino-Tibetan languages were grouped into major lingu...
For the Castorimorpha clade we tested the following alternative tree topologies. Retroposon markers with pattern 1 – mouse(+)/beaver(+)/kangaroo rat(−)/outgroups(−) would indicate a close relationship between the mouse and the beaver to the exclusion of the kangaroo rat. However, all ...