Computational protocol: The divorce of Sporothrix and Ophiostoma: solution to a problematic relationship

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Protocol publication

[…] Data sets of sequences derived in the present study () together with reference sequences obtained from NCBI GenBank, were compiled using MEGA 6.06 (). All datasets (LSU, ITS, BT and CAL) were aligned using an online version of MAFFT 7 () and subjected to Gblocks 0.91b () using less stringent selection options, to eliminate poorly aligned positions and divergent regions from subsequent phylogenetic analyses. All datasets obtained from Gblocks were subjected to Maximum Likelihood (ML) and Bayesian Inference (BI) analyses. ML analyses using RaxML () were conducted with raxmlGUI 1.3 () with 10 runs using the GTRGAMMA substitution model and 1 000 bootstraps each. BI analyses were conducted with MrBayes 3.2.5 () with 10 runs using the GTRGAMMA substitution model, and 5 M generations each with tree sampling every 100th generation. Bayesian posterior probabilities were calculated for each dataset after discarding 25% of the trees sampled as prior burn-in. […]

Pipeline specifications

Software tools MEGA, MAFFT, Gblocks, RAxML, raxmlGUI, MrBayes
Application Phylogenetics
Organisms Homo sapiens, Sporothrix schenckii, Treponema pallidum
Diseases Sporotrichosis