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pangenes/README.md

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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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- [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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taken from [GET_HOMOLOGUES](http://eead-csic-compbio.github.io/get_homologues/manual).
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Accessory genes include both shell and cloud genes.*
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This 30min [video](https://www.youtube.com/watch?v=JcxQ97TzzzQ) introduces GET_HOMOLOGUES, GET_HOMOLOGUES-EST
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and GET_PANGENES.
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## Definition of pangene
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According to our paper <https://doi.org/10.1186/s13059-023-03071-z>, a `pangene` can be defined as follows:
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## [Command line demo]
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Please check this [asciinema step-by-step demo](https://asciinema.org/a/W7xVe1112Fl8BImRB5ZW2MWE7) on how to install and run GET_PANGENES on a Debian/Ubuntu linux system.
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Please check this [asciinema step-by-step demo](https://asciinema.org/a/W7xVe1112Fl8BImRB5ZW2MWE7)
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on how to install and run GET_PANGENES on a Debian/Ubuntu linux system.
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<!--
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asciinema rec -t "GET_PANGENES tutorial" get_pangenes.cast

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