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Protocol publication

[…] For phylogenetic analysis, full-length amino acid sequences and vertebrate mRNA sequences were analyzed. A reciprocal BLAST hit analysis was performed with the EEVS protein (see ). Sequences were aligned using MUSCLE. ProtTest was used to determine the best model of protein evolution (LG+G) (), and MEGA6 was used to determine the best fit nucleic acid evolutionary model (K80+G) (). RAxML was used for maximum likelihood analysis, and the robustness of the trees was assessed by bootstrap analysis (1000 replicates) (). Bayesian analysis was performed by MrBayes (version 3.2.3), using a random starting tree, running eight chains for 4,000,000 generations, sampling every 250 trees (). The first 5000 trees were discarded as the burnin, with the remaining trees used to calculate posterior probability. RAxML and MrBayes were run on the CIPRES science gateway (). MEGA6 was used for maximum likelihood analysis of vertebrate mRNA sequences with tree robustness assessed by bootstrap (500 replicates). Sources of proteins for the analyses are listed in . […]

Pipeline specifications

Software tools ProtTest, MEGA, RAxML, MrBayes
Application Phylogenetics
Organisms Saccharomyces cerevisiae