Jul 26, 2020
AMOVA AND PHILOGENY IN HIV-1 PROTOCOLS
- 1LaBECom
Protocol Citation: Pierre PhD Teodosio 2020. AMOVA AND PHILOGENY IN HIV-1 PROTOCOLS. protocols.io https://dx.doi.org/10.17504/protocols.io.bixqkfmw
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: July 23, 2020
Last Modified: July 26, 2020
Protocol Integer ID: 39632
METHODOLOGY
METHODOLOGY
DATABANK: The 153 gene sequences of the integrase gene of human immunodeficiency virus 1 were collected from GENBANK (https://www.ncbi.nlm.nih.gov/popset/?term=MN888087.1 and participate in a PopSet dipped by Totmenin and collaborators on March 25, 2020 (Popset:1822236350).
PHYLOGENETICS ANALYSES: For phylogenetic analyses, the previously described nucleotide sequences were used. The sequences were aligned using the MEGA X program (TAMURA et al., 2018) and gaps were extracted for the construction of phylogenetic trees.
GENETIC STRUCTURING ANALYSES: Paired FST estimators were obtained with the software Arlequin v. 3.5 (EXCOFFIER et al., 2005) using 1000 random permutations. The FST matrix generated by the software was used in the construction of a dendrogram based on the UPGMA distance method with the MEGA X software (TAMURA et al., 2018) and the FST and geographic distance matrices were not compared.