PhyloPhlAn for partial sequence

I am trying to determine the classification of partial viral sequences by creating a phylogenetic tree using sequences from a viral genus and then determining the classification of a query sequence through intraclade distances as described in ‘PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes’ by Segata et. al.

Which tutorial is most suitable?

Hello and thanks for your interest in PhyloPhlAn.

Unfortunately, we don’t have a tutorial with a viral example, as we developed PhyloPhlAn to be automatic for microbes.
Nonetheless, you can manually tune some parameters and manually change the configuration file to be able to work with viral sequences (in particular for the model to be used for the phylogeny reconstruction).
I’m not an expert on viruses so I can’t really help you here about the right parameters to tune and modify.

Many thanks,