Author: Maciej F Boni; Philippe Lemey; Xiaowei Jiang; Tommy Tsan-Yuk Lam; Blair Perry; Todd Castoe; Andrew Rambaut; David L Robertson
Title: Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic Document date: 2020_3_31
ID: h2uc7ria_39
Snippet: First, we took an approach that relies on identifying mosaic regions (via 3SEQ) that are also supported by phylogenetic incongruence (PI) signals (Boni et al., 2010) . As 3SEQ is the most powerful the mosaic methods (Boni et al., 2007) , we used 3SEQ to identify the best supported breakpoint history for each potential child (recombinant) sequence in the data set. A single 3SEQ run on the genome alignment resulted in 67 out of 68 sequences support.....
Document: First, we took an approach that relies on identifying mosaic regions (via 3SEQ) that are also supported by phylogenetic incongruence (PI) signals (Boni et al., 2010) . As 3SEQ is the most powerful the mosaic methods (Boni et al., 2007) , we used 3SEQ to identify the best supported breakpoint history for each potential child (recombinant) sequence in the data set. A single 3SEQ run on the genome alignment resulted in 67 out of 68 sequences supporting some recombination in the past, with multiple candidate breakpoint ranges listed for each putative recombinant. Then, we (a) collected all breakpoints into a single set, (b) complemented this set to generate a set of non-breakpoints, (c) grouped the non-breakpoints into contiguous breakpoint-free regions (BFRs), and (d) sorted these regions by length. A phylogenetic tree -using RAxML v8.2.8 (Stamatakis, 2014 (Stamatakis, , 2006 , GTR+Γ model, 100 bootstrap replicates -was inferred for each BFR longer than 500nt.
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