What it does

Creation of a multiple alignment of OTUs with PyNAST (if you have an alignment template file) or with Mafft (if you have not an aligned template file). And creation of a phylogenetic tree with FastTree.

Inputs/Outputs

Input

OTUs fasta file:

The OTUs sequence file (format FASTA). Careful: FROGS Tree works only with less than 10 000 sequences!

(optional) Template alignment file:

A pre-aligned database of sequences (the “template” sequence) (format multiple alignement).

OTUs biom file:

The OTUs biom file (format biom1). This file can be obtained in particular with the FROGS pipeline.

Outputs

Newick file (tree.nwk):

The phylogenetic tree in Newick format (format nxh).

Html file (summary.html):

The summary file describing which OTUs are contained or not in the phylogenetic tree (format HTML).

Contact

Contacts: frogs@inra.fr

Repository: https://github.com/geraldinepascal/FROGS

Please cite the FROGS Publication: Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA , http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf

Depending on the help provided you can cite us in acknowledgements, references or both.