Author: Hayward, Joshua A; Tachedjian, Mary; Cui, Jie; Cheng, Adam Z; Johnson, Adam; Baker, Michelle L; Harris, Reuben S; Wang, Lin-Fa; Tachedjian, Gilda
Title: Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity Document date: 2018_3_29
ID: 1i6c0l3e_33
Snippet: The identities of the putative bat A3 gene products were confirmed by phylogenetic analysis. All reference sequences were downloaded from Ensembl (https://www.ensembl.org/; last accessed April 3, 2018) and aligned with P. alecto sequences using MUSCLE (Edgar 2004 ). Regions of low conservation and uncertain alignment were removed using the Gblocks program (Talavera and Castresana 2007) . Phylogenetic relationships were inferred using the maximum .....
Document: The identities of the putative bat A3 gene products were confirmed by phylogenetic analysis. All reference sequences were downloaded from Ensembl (https://www.ensembl.org/; last accessed April 3, 2018) and aligned with P. alecto sequences using MUSCLE (Edgar 2004 ). Regions of low conservation and uncertain alignment were removed using the Gblocks program (Talavera and Castresana 2007) . Phylogenetic relationships were inferred using the maximum likelihood (ML) method available in the MEGA6 program (Tamura et al. 2013) , employing nearest-neighbor interchange and branch swapping, and the best-fit model of amino acid substitution was found to be JTT þ G (Tamura et al. 2013) . To determine the robustness of each node 1,000 bootstrap replications were incorporated.
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