Papillomavirus super-pangenome (Li et al., 2025)

[Paururo]

Recording a use of get_MNV that none of us here were involved in, since the
point of this category is to collect them wherever they happen.

The work
Super-pangenome analysis of 3562 human and animal papillomavirus isolates
illuminates their genome and pathogenicity evolution
Li H, Chen J, Zhang X, Zhang X, Yang L, Ding Y, Chen C, Shuai Y, Song M, Liu J,
Feng L, Li J, Yue J-X. bioRxiv, preprint, v2 (2025).
DOI: 10.1101/2025.07.20.664904

Version used: get_MNV v1.0.0, cited by its GitHub URL.

Organism: human and animal papillomaviruses, 3562 isolates.

What it was used for

In their variant analysis, after filtering by allele frequency between risk
groups, they reach the case of several variant sites landing in the same codon.
get_MNV is the step that identifies those and relabels the amino acid change
accordingly. That output then feeds branch- and site-specific selection analysis
with aBSREL from HyPhy.

So it is used exactly where the tool is meant to be used, and as a preparatory
step rather than as an end in itself: the selection analysis downstream is only
as good as the amino acid labels going into it.

Two notes for anyone doing something similar

Version 1.0.0 is from October 2024, and a fair amount has changed since,
including read-backed support for whether two changes in a codon actually travel
on the same molecule. Anyone repeating this kind of analysis may want the current
release; the codon-level relabelling used here works the same way.

If any of the authors find this, corrections are welcome, and so is anything that
was awkward.