When we look at taxonomy, there are multiple “modes” of classification. There is “folk taxonomy” in which organisms are grouped into categories such as “bugs,” “lizards,” “shrubs,” “trees,” “snakes,” “worms,” etc. These are taxa based upon form or external physical characteristics, usually without any specific characteristics, but general “reactions” to the organism. I am, in no way, saying this is a scientific method of taxonomy, but it is often confused as such. “Trees” and “shrubs” are not two scientifically distinct taxa. The Crape Myrtle, for example, can be considered both. Lythraceae, the evolutionary family to which the Crape Myrtle belongs, encompasses everything from herbs to shrubs to trees (in folk taxonomy). This is strange because a “tree” can be one of many different families, with each family having other types of plants as well.
Modern taxonomy relies heavily upon numerous specific traits such as (in mammals) the ear bones, finger bones, mandibular bones or (in modern organisms) embryological development and (in plants) leaf arrangement and venation, stem structure, reproductive attributes, etc. Taxonomy is the way in which species are organized based upon these traits. This may (and usually does) coincide with the phylogeny. A single organism can be integrated into taxonomy without analysis of any other organisms. An accurate phylogeny requires comparison to other related species. The taxonomy of an organism is the same regardless of related organisms. The phylogeny is how these organisms are related to related organisms. A phylogeny places an organism in evolutionary context. A good argument can be made that a good taxonomy also does this, but functional (trees, herbs, shrubs, venomous snakes, nonvenomous snakes, etc.) groups can also be quite useful in guide books or layman references. These frequently do not coincide with natural taxa.