Skip to content

Phylogenetic: Create phylogenetic trees between recombination breakpoints#42

Draft
j23414 wants to merge 11 commits into
mainfrom
vp1_rdrp
Draft

Phylogenetic: Create phylogenetic trees between recombination breakpoints#42
j23414 wants to merge 11 commits into
mainfrom
vp1_rdrp

Conversation

@j23414

@j23414 j23414 commented Oct 31, 2025

Copy link
Copy Markdown
Contributor

Description of proposed changes

Norovirus genome has known breakpoints between ORF1-ORF2 (crosses the RdRp-VP1 boundary) and ORF2-ORF3. Ergo it may make more sense and reduce the number of trees if we focus on the non-recombining regions for phylogenetic trees.

Only building time trees within a genotype (e.g. GII.2) allows for time inference. Otherwise, the all trees are too diverged to get a reasonable inference and should only be produced as divergence trees.

From test run: https://github.com/nextstrain/norovirus/actions/runs/18925586046

group ORF1 ORF2 ORF3 RdRp VP1
GII.2 ORF1 ORF2 ORF3 RdRp VP1
GII.3 ORF1 ORF2 ORF3 RdRp VP1
GII.4 ORF1 ORF2 ORF3 RdRp VP1
GII.6 ORF1 ORF2 ORF3 RdRp VP1
GII.17 ORF1 ORF2 ORF3 RdRp VP1

Related issue(s)

Checklist

  • Checks pass
  • Update changelog

@j23414 j23414 force-pushed the vp1_rdrp branch 3 times, most recently from d4da737 to 356c5eb Compare November 8, 2025 00:22
@j23414 j23414 changed the title [WIP] Phylogenetic: Create phylogenetic trees between recombination breakpoints Phylogenetic: Create phylogenetic trees between recombination breakpoints Nov 20, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants