Selected article for: "LG substitution matrix and recombination breakpoint"
Author: Maddamsetti, Rohan; Johnson, Daniel T.; Spielman, Stephanie J.; Petrie, Katherine L.; Marks, Debora S.; Meyer, Justin R.
Title: Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature
  • Document date: 2018_9_11
    • ID: z7alrc7s_11
    Snippet: We used FastTree (Price et al. 2010) with an LG substitution matrix (Le and Gascuel 2008) to generate approximately maximum-likelihood phylogenies. To account for recombination when estimating site-specific evolutionary rates in the specificity region, we first ran a modified SBP algorithm on the specificity region (Kosakovsky Pond et al. 2006 ). We found a putative recombination breakpoint at alignment position 49, supported by Akaike's informat.....
    Document: We used FastTree (Price et al. 2010) with an LG substitution matrix (Le and Gascuel 2008) to generate approximately maximum-likelihood phylogenies. To account for recombination when estimating site-specific evolutionary rates in the specificity region, we first ran a modified SBP algorithm on the specificity region (Kosakovsky Pond et al. 2006 ). We found a putative recombination breakpoint at alignment position 49, supported by Akaike's information criterion but not the Bayesian information criterion. We therefore partitioned the specificity region at position 49 and recalculated trees for each partition using FastTree with an LG substitution matrix. We next calculated site-specific evolutionary rates with LEISR (Spielman and Kosakovsky Pond 2018), a scalable implementation of Rate4Site (Pupko et al. 2002) that accounts for recombination breakpoints. We ran LEISR using an LG substitution matrix.

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