Computational protocol: A new species and a new record of Laccaria (Fungi, Basidiomycota) found in a relict forest of the endangered Fagusgrandifoliavar.mexicana

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Protocol publication

[…] The phylogenetic analysis was performed with the sequences obtained in this study, as well as some retrieved from GenBank (http://www.ncbi.nlm.nih.gov/) derived from the Blast analysis (only those that best match), and complemented with related sequences used by , and (Table ). For this purpose, we constructed a dataset (ITS+LSU) using PhyDE v.0.9971 (), also with MEGA 6.06 () calculated the best evolutionary model and constructed the phylogenetic tree under the method of Maximum Likelihood (ML) with 500 bootstrap replications, and finally with MrBayes v 3.2.6 () constructed the phylogenetic tree (as ) under the method of Bayesian Inference (BI). The phylogenies from ML and BI analyses were displayed using Mega 6.06 and FigTree v1.4.3 () respectively. […]

Pipeline specifications

Software tools MEGA, MrBayes, FigTree
Application Phylogenetics