[med-svn] [Git][med-team/gubbins][upstream] New upstream version 3.3

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / gubbins


Commits:
c3ba1c52 by Andreas Tille at 2023-02-07T10:04:38+01:00
New upstream version 3.3
- - - - -


30 changed files:

- + .github/workflows/build.yml
- − .travis.yml
- CHANGELOG.md
- − Dockerfile
- − GubbinsManual_latest.docx
- Makefile.am
- + R/scripts/treeWAS_run.R
- README.md
- VERSION
- + codecov.yml
- configure.ac
- + docs/gubbins_manual.md
- + docs/gubbins_tutorial.md
- + docs/pmen3_output.png
- + environment.yml
- example_data/PMEN1/PMEN1.branch_base_reconstruction.embl
- example_data/PMEN1/PMEN1.filtered_polymorphic_sites.fasta
- example_data/PMEN1/PMEN1.filtered_polymorphic_sites.phylip
- example_data/PMEN1/PMEN1.final_tree.tre
- + example_data/PMEN1/PMEN1.log
- + example_data/PMEN1/PMEN1.node_labelled.final_tree.tre
- − example_data/PMEN1/PMEN1.node_labelled.tre
- example_data/PMEN1/PMEN1.per_branch_statistics.csv
- example_data/PMEN1/PMEN1.recombination_predictions.embl
- example_data/PMEN1/PMEN1.recombination_predictions.gff
- example_data/PMEN1/PMEN1.summary_of_snp_distribution.vcf
- + example_data/PMEN1/PMEN1_output.png
- example_data/PMEN1/README.md
- example_data/ST239/README.md
- example_data/ST239/ST239.branch_base_reconstruction.embl


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/commit/c3ba1c5251fbd2065bb1217b791ddace027cce14

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View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/commit/c3ba1c5251fbd2065bb1217b791ddace027cce14
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