Impact of Phylogenetic Method Choice on Indel Analyses in HIV-1 Subtype B.

ABSTRACT: Insertions and deletions (indels) play a critical role in the evolutionary dynamics of genomes, yet their accurate detection and interpretation in phylogenetic studies remain challenging. Our study investigates the influence of different multiple sequence alignment (MSA) and ancestral sequence reconstruction (ASR) tools on indel pattern reconstruction, focusing on HIV-1 subtype B. We aim to understand how methodological choices affect the detection of indels, thereby emphasizing the importance of selecting appropriate tools for evolutionary analyses to improve phylogenetic accuracy. We conducted a comparative analysis using five MSA tools (MAFFT, PRANK+F, IndelMaP, ProPIP, and Historian) and five ASR tools (GRASP, FastML, IndelMaP, ARPIP, and Historian). By examining inferred indel events

SUBMITTER: Seppey M 

PROVIDER: S-EPMC12188288 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature