phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
In my Eukaryotic metagenome dataset, it is impossible to identify most samples to species level or to cluster them in OTUs. I have many reads that are for example only identified to class or phylum level. Is it possible to actually use the full abundance table with all reads (so e.g. including class, species, order, phylum,..), and have analyses that take into account the taxonomy and taxonomic level to which the reads are identified? For example in an ordination plot? Or is the only way to select a taxonomic rank per analysis?
In my Eukaryotic metagenome dataset, it is impossible to identify most samples to species level or to cluster them in OTUs. I have many reads that are for example only identified to class or phylum level. Is it possible to actually use the full abundance table with all reads (so e.g. including class, species, order, phylum,..), and have analyses that take into account the taxonomy and taxonomic level to which the reads are identified? For example in an ordination plot? Or is the only way to select a taxonomic rank per analysis?