Computational protocol: Four Unrecorded Wood Decay Fungi from Seoul in Korea

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Protocol publication

[…] The DNAs from specimens were extracted, after which internal transcribed spacer (ITS) and nuclear large subunit ribosomal DNA (nuc-LSU) sequences were obtained using the primer sets ITS1F/ITS4, ITS1F/ITS4B, or ITS5/ITS4 for the ITS region [, ] and LR0R/LR3 or LR0R/LR5 for the nuc-LSU region [], according to Jang et al. []. The sequences obtained in this study were deposited under GenBank accession Nos. JX463652~JX463663. Each sequence was compared to the reference sequences in GenBank, NCBI using a BLAST search (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Each sequence was aligned with those obtained from GenBank using MAFFT 6.884 [] by following the L-INS-i method and manually edited using MacClade 4.08 []. For analysis, each dataset from each species was treated separately. Bayesian analyses were performed with MrBayes 3.2.1 []. The best-fit model for each dataset was selected by MrModeltest 2.3 (AIC) []. Two independent runs with 1,000,000 generations were performed, with sampling of every 100th generation. The first 25% of the trees was discarded while the last 75% of the trees was used to construct consensus trees. We also checked the graphic representation of the likelihood scores of the sampled trees. Potential scale reduction factors were close to 1.0 for all parameters. A 50% majority-rule consensus tree for each dataset was constructed, and tree reliability was assessed by posterior probability. […]

Pipeline specifications

Software tools MAFFT, MacClade, MrBayes, MrModelTest
Application Phylogenetics