Selected article for: "amino acid and automatically generate"
Author: Rohan Maddamsetti; Daniel T. Johnson; Stephanie J. Spielman; Katherine L. Petrie; Debora S. Marks; Justin R. Meyer
Title: Viral gain-of-function experiments uncover residues under diversifying selection in nature
  • Document date: 2018_1_3
    • ID: gqhlw20n_21
    Snippet: We used RAxML 31 to generate maximum-likelihood phylogenies using automatically selected amino acid substitution matrices (PROTGAMMAAUTO) based on model fit. To account for recombination when estimating site-specific evolutionary rates in the specificity region, we first ran a modified SBP algorithm 32 on the specificity region. We found a putative recombination breakpoint at residue 1000, supported by Akaike's information criterion but not the B.....
    Document: We used RAxML 31 to generate maximum-likelihood phylogenies using automatically selected amino acid substitution matrices (PROTGAMMAAUTO) based on model fit. To account for recombination when estimating site-specific evolutionary rates in the specificity region, we first ran a modified SBP algorithm 32 on the specificity region. We found a putative recombination breakpoint at residue 1000, supported by Akaike's information criterion but not the Bayesian information criterion. We therefore partitioned the specificity region at residue 1000 and re-calculated trees for each partition using FastTree 33 with an LG substitution matrix 34 .

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