Computational protocol: Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences

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Protocol publication

[…] ClustalX Multiple Sequence Alignment programme was used to align DNA sequences using the default settings. Sarracenia flava was designated as the outgroup in the phylogenetic analyses. The DNA sequences of the ITS region and trnL intron were combined in phylogenetic analyses. The evolutionary history was analyzed by neighbor-joining (NJ) and maximum parsimony (MP) methods using PAUP* 4.0b10 []. All positions containing gaps and missing data were removed from the dataset using the ‘complete deletion’ option. The pairwise distances generated using the uncorrected “p” model were used to construct the NJ tree. For the MP analysis, the cladograms were constructed utilizing unordered parsimony with equal weight. A heuristic search was conducted with the tree bisection–reconnection (TBR) branch swapping algorithm, random stepwise addition and ‘Mul-Trees’ option set on all the characters were weighted equally. The internal branch supports for the NJ and MP trees were assessed with Bootstrap analyses using 500 replicates. Bayesian inferences were carried out [, ] using MrBayes 3.12 []. The general reversible model with Gamma distributed rate heterogeneity (GTR + G) was selected by AIC using MrModelTest version 2.2 []. Two simultaneous metropolis-coupled Monte-Carlo Markov chains for >1,000,000 generations, a sample frequency of 100 generations and average standard deviation of split frequencies 0.009311 was used in Bayesian inference. […]

Pipeline specifications

Software tools Clustal W, PAUP*, MrBayes, MrModelTest
Application Phylogenetics
Organisms Nocardiopsis alba