Workflow for alignment dataset generation and phylogenetic analysis.

<p>(A) The process begins with a downloaded, filtered near full-length (nFL) HIV-1 subtype B genome alignment as input. (B) To generate multiple alignment samples, the order of taxa within the input alignment is randomly shuffled. (C) For each shuffled sample, various datasets are created by m...

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Bibliographic Details
Main Author:	August Guang (9975678) (author)
Other Authors:	Casey W Dunn (21263816) (author), Vlad Novitsky (3366560) (author), Mark Howison (3315450) (author), Rami Kantor (7863) (author)
Published:	2025
Subjects:	Genetics Molecular Biology Biotechnology Evolutionary Biology Cancer Statistics Infectious Diseases Virology Biological Sciences not elsewhere classified still broadly used mean cluster size compared tree similarity also decreased number shape alignment provides flexible approach called larger clusters identified partial pol sequences 1 near full improve phylogenetic inference long hiv sequences phylogenetic inference near full 1 sequences shape alignments pol regions new approach molecular clusters improve phylogenetic full dataset short sequences long sequences available sequences xlink "> transmission dynamics systematically masked subset dataset study subset straightforward method short hiv shaped alignments results suggest provide insights proportional increments missing characters immediately depending different lengths analysis goals
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Workflow for alignment dataset generation and phylogenetic analysis.

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