@@ -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.
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>`.