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README.md

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PanPhlAn is written in Python and covers the 4 main tasks:
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* `panphlan_download_pangenome.py`, to download pangenome files (fasta, BowTie2 indexes and general information) for over 3,000 species
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For custom pangenome generation (advanced) see the [PanPhlAn exporter](https://github.com/SegataLab/PanPhlAn_pangenome_exporter)
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* `panphlan_map.py`, to profile each metagenomic sample by mapping it against the species of interest
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* `panphlan_profile.py`, to merge and process the mapping results in order to get the final gene presence/absence matrix
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* `panphlan_find_gene_grp.py`, organise OPTICS clustering to find some group of gene with similar profile and assess if they could be mobile elements in the genome. Also plot the presence/absence matrix as Heatmap.

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