#
iqtree2
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This repository contains a set of scripts and workflows designed to search for Respiratory Complex I (NADH Ubiquinone Oxidoreductase) subunits in prokaryotic genomes and proteomes.
bioinformatics biopython protein-sequences proteome homology-search mafft mmseqs2 fasttree prokaryotic-genomes hmmer3 species-distribution evalue-thresholds alphafold2 operons iqtree2 protein-sequences-tree
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Updated
Mar 23, 2026 - Jupyter Notebook
Graph-based pangenomic and synteny analysis of Helicobacter pylori (n=41 complete RefSeq genomes) using PPanGGOLiN, with reproducible workflows for annotation (Prokka), ANI quality control (FastANI), core-genome phylogeny (MAFFT + IQ-TREE 2), resistome profiling (AMRFinderPlus), and publication-grade visualizations.
bioinformatics microbial-genomics comparative-genomics synteny phylogenomics pangenomics mafft resistome prokka fastani bacterial-genomics amrfinderplus iqtree2 helicobacter-pylori ppanggolin
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Updated
Apr 6, 2026 - Shell
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