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Bootstrap percentage values (50%) generated from 1,000 replicates from maximum parsimony and posterior probabilities (>80%) from Bayesian analysis are shown as [Maximum parsimony bootstrap value/Bayesian posterior probabilities].
Strain M27053 was closely related to strain bt31 with 100% support from the Bayesian posterior probability and 72% support from maximum parsimony bootstrap.
Robustness of individual branches was estimated by maximum parsimony bootstrap proportions (BP), using 500 replicates, each consisting of a heuristic search with 50 random taxon addition sequences, MAXTREES set to autoincrease, and TBR branch swapping.
In separate and combined analyses of nuclear ribosomal RNA genes (rDNA) and translated rpb2 (RPB2) sequences using Bayesian, maximum likelihood (ML) and maximum parsimony (MP) methods (BPP = Bayesian Posterior Probabilities, MLB = Maximum Likelihood Bootstrap, MPB = Maximum Parsimony Bootstrap), we recovered species relationships that are congruent with previous molecular phylogenies [17].
Maximum parsimony bootstrap analysis was performed with 1000 resamplings.
Maximum Parsimony bootstrap analyses were carried out with the same settings and with 1000 replicates.
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We cannot explain why FGB-int7 provides a division not seen in any other data set but this division is based on fewer than 25 nucleotide sites (approximately 2% of their data), and the monophyly of these two clades were supported by only 85% and 60% of maximum parsimony bootstraps.
The ML tree with bootstrap (BS) percentages above each branch and the maximum parsimony (MP) bootstrap (BS) percentages below each branch is presented in Figure 2 and 3.
For Maximum Parsimony each bootstrap replicate consisted of a full heuristic search with 10 stepwise-addition random replicates and TBR branch swapping.
For one analysis this was highly significant (maximum parsimony - bootstrap 94%).
In addition, we did an unweighted maximum parsimony (MP) bootstrap analysis of the data.
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