Main tool: Gubbins
Code repository: https://github.com/nickjcroucher/gubbins
Additional tools installed via micromamba:
Name Version Build Channel
───────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
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gubbins 3.4.1 py310pl5321h577a1d6_0 bioconda
gxx_impl_linux-64 15.1.0 h6a1bac1_4 conda-forge
harfbuzz 11.4.3 h15599e2_0 conda-forge
icu 75.1 he02047a_0 conda-forge
iqtree 3.0.1 h503566f_0 bioconda
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python 3.10.18 hd6af730_0_cpython conda-forge
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r-ggplot2 3.5.2 r44hc72bb7e_0 conda-forge
r-ggplotify 0.1.2 r44hc72bb7e_1 conda-forge
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r-memoise 2.0.1 r44hc72bb7e_3 conda-forge
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r-ragg 1.4.0 r44hdcc764c_0 conda-forge
r-rappdirs 0.3.3 r44hb1dbf0f_3 conda-forge
r-rcolorbrewer 1.1_3 r44h785f33e_3 conda-forge
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r-rematch 2.0.0 r44hc72bb7e_1 conda-forge
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r-tibble 3.3.0 r44h2b5f3a1_0 conda-forge
r-tidyr 1.3.1 r44h0d4f4ea_1 conda-forge
r-tidyselect 1.2.1 r44hc72bb7e_1 conda-forge
r-tidytree 0.4.6 r44hc72bb7e_1 conda-forge
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r-viridislite 0.4.2 r44hc72bb7e_2 conda-forge
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rapidnj 2.3.2 h9948957_6 bioconda
raxml 8.2.13 h7b50bb2_3 bioconda
raxml-ng 1.2.2 h6747034_2 bioconda
readline 8.2 h8c095d6_2 conda-forge
scipy 1.13.1 py310h93e2701_0 conda-forge
sed 4.9 h6688a6e_0 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
ska2 0.4.1 h4349ce8_0 bioconda
sysroot_linux-64 2.34 h087de78_2 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tktable 2.10 h8d826fa_7 conda-forge
tzdata 2025b h78e105d_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forgeBasic information on how to use this tool:
- executable:
run_gubbins.py - help:
-h - version:
--version - description: Gubbins detects recombinations through the locally elevated densities of polymorphisms that arise when sequence segments are acquired from a donor genetically divergent from the set of analyzed sequences.
Full documentation: https://github.com/nickjcroucher/gubbins/blob/master/docs/gubbins_manual.md
run_gubbins.py fasta_alignment.aln