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- [ Definition of pangene] ( #definition-of-pangene )
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- [ Command line demo] ( #command-line-demo )
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- [ How it works] ( #how-it-works )
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- - [ Runmodes and HPC configuration] ( #runmodes-and-hpc-configuration )
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- [Transformation of gene coordinates](#transformation-of-gene-coordinates)
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- [Overlap calculation](#overlap-calculation)
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- [Pairwise genome comparisons](#pairwise-genome-comparisons)
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- [From pairs of genes to clusters](#from-pairs-of-genes-to-clusters)
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- [Parameters](#parameters)
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- [Dependencies and installation](#dependencies-and-installation)
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+ - [Runmodes and HPC configuration](#runmodes-and-hpc-configuration)
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- [Command-line options](#command-line-options)
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- [Input file format](#input-file-format)
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- [ Example 1: default core pangene set analysis] ( #example-1-default-core-pangene-analysis-and-hpc-settings )
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