Phynteny predicts the functions of unknown phage genes from gene order (synteny)

Phynteny is an open-source tool from the Edwards Lab (Grigson et al.) that uses a long short-term memory (LSTM) model trained on phage synteny, the conserved gene order across phages, to assign hypothetical phage proteins to a PHROG functional category; about 65% of phage genes have no known function. It takes a GenBank file with PHROG annotations (for example from pharokka) and returns predictions with a Phynteny score and a recalibrated confidence score, and it installs from bioconda or PyPI. The README flags this LSTM version as a work in progress limited to phages with 120 genes or fewer and points to a newer Phynteny Transformer.