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Here, we provide a fully functional copy of phenotrex models for phenotype prediction to the scientific community. Please follow these instructions:

1. Get and install the phenotrex software from https://github.com/univieCUBE/phenotrex

2. Download and extract the models from http://fileshare.csb.univie.ac.at/phenotrex/latest/classifier.tar.gz. New releases of the models are announced in our release newsletter. Please subscribe to stay informed. For updating models, just remove the old models folder and download and extract the new one.

3a. To predict phenotypic traits for genomes and metagenomic bins, each of them needs to be transformed into a list of eggNOG 5.0 taxonomy-level 2 IDs, which are present in the genome. At the moment, we recommend HMMER3 hmmscan on the bactNOG Hidden Markov Models with an e-Value threshold of 0.01.

3b. Alternatively phenotrex is also able to use a novel super fast EggNOG5 annotation tool called DeepNOG (Feldbauer et al. 2020, in print). It is necessary to use DeepNOG specific phenotrex models from here: http://fileshare.csb.univie.ac.at/phenotrex/latest/deepnog_classifier.ta....

4. Single or multiple genotype profiles can be stored in one tab delimited text file, one genome per line, including a brief header to inform phenotrex about the features used:

#feature_type:eggNOG5-tax-2
genomeid1	ENOG23444	ENOG42335	ENOG34345	................etc
genomeid2	ENOG23448	ENOG42339	ENOG34340	................etc

5.After the list of bactNOGs has been created for each genome, run predictions model by model, e.g.:

<path_to_phenotrex>/phenotrex predict --classifier <modelpath>/AOB.svm.class --genotype <genotype_file></genotype_file></modelpath></path_to_phenotrex>

In case of problems, please do not hesitate to contact us: contact.cube@univie.ac.at. We are more than happy to help you and will continuously improve this website.