Skip to content
Snippets Groups Projects
Commit 025c058e authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

More precise definition of external dependencies

parent a5fc313d
No related branches found
No related tags found
No related merge requests found
Pipeline #38179 passed with warnings
......@@ -46,11 +46,12 @@ Amandine PERRIN, Eduardo P.C. ROCHA (2020). PanACoTA: A modular tool for massiv
PanACoTA is written in **python3**. So, you need python3 (and pip3 for installation) to run it.
Its external dependencies are:
- [**prokka**](https://github.com/tseemann/prokka) and/or [**prodigal**](https://github.com/hyattpd/Prodigal) (for 'annotate module' - to uniformly annotate your genomes)
- [**mmseqs**](https://github.com/soedinglab/MMseqs2) ('pangenome module' - to generate pangenomes)
- [**mafft**](http://mafft.cbrc.jp/alignment/software/) ('align module' - to align persistent genome)
- At least one of those softwares, to infer a phylogenetic tree ('tree module'):
PanACoTA has several dependencies. Install only the one(s) you need, according to the module you want to use:
- For prepare module: [**mash**](https://mash.readthedocs.io/en/latest/) (to filter genomes)
- For annotate module: [**prokka**](https://github.com/tseemann/prokka) and/or [**prodigal**](https://github.com/hyattpd/Prodigal) (to uniformly annotate your genomes)
- For pangenome module: [**mmseqs**](https://github.com/soedinglab/MMseqs2) (to generate pangenomes)
- For align module: [**mafft**](http://mafft.cbrc.jp/alignment/software/) (to align persistent genome)
- For tree module: At least one of those softwares, to infer a phylogenetic tree:
- [**IQ Tree**](http://www.iqtree.org/)
- [**FastTreeMP**](http://www.microbesonline.org/fasttree/#Install): We advise to download C code, and compile as described here above.
- [**FastME**](http://www.atgc-montpellier.fr/fastme/binaries.php)
......
......@@ -13,10 +13,11 @@ Dependencies
There are several external dependencies, and you can install only the ones you need for your study:
- `prokka <https://github.com/tseemann/prokka>`_ and/or `prodigal <https://github.com/hyattpd/Prodigal>`_ (for 'annotate module' - to uniformly annotate your genomes)
- `mmseqs <https://github.com/soedinglab/MMseqs2>`_ ('pangenome module' - to generate pangenomes)
- `mafft <http://mafft.cbrc.jp/alignment/software/>`_ ('align module' - to align persistent genome)
- At least one of those softwares, if you want to infer a phylogenetic tree ('tree module'):
- For prepare module: `mash <https://mash.readthedocs.io/en/latest/>`_ (to filter genomes)
- For annotate module: `prokka <https://github.com/tseemann/prokka>`_ and/or `prodigal <https://github.com/hyattpd/Prodigal>`_ (to uniformly annotate your genomes)
- For pangenome module: `mmseqs <https://github.com/soedinglab/MMseqs2>`_ (to generate pangenomes)
- For align module: `mafft <http://mafft.cbrc.jp/alignment/software/>`_ (to align persistent genome)
- For tree module: At least one of those softwares:
- `IQtree <http://www.iqtree.org/>`_
- `FastTreeMP <http://www.microbesonline.org/fasttree/#Install>`_: We advise to download C code, and compile as described :ref:`here above <fasttree>`.
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment