Computational protocol: The genus Parasola in Pakistan with the description of two new species

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Protocol publication

[…] ITS, 28S and TEF1α sequences were aligned using BIOEDIT v 7.2.5 () and CLUSTAL X 2.1 (). The ITS, 28S and TEF1α alignments were concatenated into a supermatrix. Psathyrella candolleana (Fr.) Maire was selected as outgroup. Alignments are submitted to TreeBase (Treebase ID 21639). Phylogenetic inference was conducted using Bayesian and Maximum Likelihood (ML) methods. For Bayesian inference, we used BEAST 1.6.2 () with a Markov chain Monte Carlo (MCMC) coalescent approach. A Yule tree prior () was used in all simulations, and the starting tree was randomly generated. Four independent runs were undertaken. Chain length was 10 million generations, with a sampling frequency of 1000. TRACER 1.6 () was used to check the effective sample size (ESS), and burn in values were adjusted to achieve an overall ESS (Effective Sample Size) of ≥ 200. Maximum clade credibility tree (20% burn-in) was generated using TREEANNOTATOR 1.6.2 (). Maximum Likelihood analyses were run in RAXML-VI-HPC (). Rapid bootstrap analysis/search for best-scoring ML tree (-f a) was configured. For the bootstrapping phase, the GTRCAT model was selected. One thousand rapid bootstrap replicates were run. Nodes were considered strongly supported when maximum likelihood bootstrap (MLB) were ≥ 70% and Bayesian posterior probability (BPP) were ≥ 0.95. […]

Pipeline specifications

Software tools BioEdit, Clustal W, BEAST, RAxML
Application Phylogenetics
Diseases Intervertebral Disc Degeneration