Selected article for: "substitution matrix and WAG substitution matrix"
Author: Drexler, Jan Felix; Corman, Victor Max; Müller, Marcel Alexander; Lukashev, Alexander N.; Gmyl, Anatoly; Coutard, Bruno; Adam, Alexander; Ritz, Daniel; Leijten, Lonneke M.; van Riel, Debby; Kallies, Rene; Klose, Stefan M.; Gloza-Rausch, Florian; Binger, Tabea; Annan, Augustina; Adu-Sarkodie, Yaw; Oppong, Samuel; Bourgarel, Mathieu; Rupp, Daniel; Hoffmann, Bernd; Schlegel, Mathias; Kümmerer, Beate M.; Krüger, Detlev H.; Schmidt-Chanasit, Jonas; Setién, Alvaro Aguilar; Cottontail, Veronika M.; Hemachudha, Thiravat; Wacharapluesadee, Supaporn; Osterrieder, Klaus; Bartenschlager, Ralf; Matthee, Sonja; Beer, Martin; Kuiken, Thijs; Reusken, Chantal; Leroy, Eric M.; Ulrich, Rainer G.; Drosten, Christian
Title: Evidence for Novel Hepaciviruses in Rodents
  • Document date: 2013_6_20
    • ID: 1v353uij_15
    Snippet: Bayesian tree topologies were assessed with MrBayes V3.1 [36] using the WAG amino acid substitution matrix and BEAST V1.7.4 [37] using the GTR model for nucleotide sequences and the FLU model for amino acid sequences. For MrBayes, two million MCMC iterations were sampled every 100 steps, resulting in 20,000 trees. For BEAST, 10,000,000 generations run under a strict clock were sampled every 1,000 steps, resulting in 10,000 trees. Burn-in was gene.....
    Document: Bayesian tree topologies were assessed with MrBayes V3.1 [36] using the WAG amino acid substitution matrix and BEAST V1.7.4 [37] using the GTR model for nucleotide sequences and the FLU model for amino acid sequences. For MrBayes, two million MCMC iterations were sampled every 100 steps, resulting in 20,000 trees. For BEAST, 10,000,000 generations run under a strict clock were sampled every 1,000 steps, resulting in 10,000 trees. Burn-in was generally 25% of tree replicates.. A human pegivirus (previously termed GBV-C1; GenBank, U36380) was used as an outgroup. Maximum Likelihood analyses were used to confirm Bayesian tree topologies using the WAG amino acid substitution model and 1,000 bootstrap replicates in PhyML [38] . Trees were visualized in FigTree from the BEAST package and Densitree [39] .

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