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--- gubbins-software [2025/05/12 12:30] – created aorth
+++ gubbins-software [2025/05/15 08:27] (current) – aorth
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 ====== gubbins ======
-Augustus predicts genes in eukaryotic genomic sequences.
+Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions, which are marked as recombinations, while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.
 ===== Information =====
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 # Only needed for build, can remove after
 $ sudo dnf install autoconf-archive.noarch libtool
+# See: https://github.com/nickjcroucher/gubbins/issues/379
+$ sed -i 's/self.executable = "iqtree"/self.executable = "iqtree2"/' python/gubbins/treebuilders.py
 $ autoreconf -i
 $ ./configure --prefix=/export/apps/gubbins/3.4