SOFT : PhyloPhlAn
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Site du soft: https://github.com/biobakery/phylophlan
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LICENSE:
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MIT license

See software documentation for more informations.

Location: /usr/local/bioinfo/src/PhyloPhlAn
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Load binaries and environment:
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-> Version 3.2.1

module load bioinfo/PhyloPhlAn/3.2.1

Help for use
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In the "PhyloPhlAn User manual", python scripts are documented, but what is used in tutorials are shell executable wrappers available in the PATH
These shell scripts are: 
- phylophlan
- phylophlan_assign_sgbs
- phylophlan_assign_sgbs_legacy
- phylophlan_draw_metagenomic
- phylophlan_get_reference
- phylophlan_patristic_distances
- phylophlan_setup_database
- phylophlan_strain_finder
- phylophlan_write_config_file
- phylophlan_write_default_configs.sh

Two python scripts are available too:
- graphlan_annotate.py
- graphlan.py

WARNING: in the example folders retrieved from github, command names are sometimes outdated, i.e. coming from older releases and replaced by new ones
In examples/03_metagenomic/run_03.sh, phylophlan_metagenomic was used, but replaced by phylophlan_assign_sgbs
This script has been corrected. Tutorials from the web pages seem more accurate.

See software documentation and our FAQ (https://vm-genoword.toulouse.inrae.fr/FAQ) for more informations.